Variant report

Variant	rs12555238
Chromosome Location	chr9:139743497-139743498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:342)
CpG islands
(count:0)
Chromatin interactive
region (count:52)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:342 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr9:139742957-139744512	GM12878	blood:	n/a	n/a
2	BCLAF1	chr9:139743431-139744162	GM12878	blood:	n/a	n/a
3	RFX5	chr9:139743155-139744336	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:139741010-139747392	GM12878	blood:	n/a	n/a
5	TCF12	chr9:139743448-139744026	A549	lung:	n/a	n/a
6	ELF1	chr9:139743472-139744471	MCF-7	breast:	n/a	n/a
7	EGR1	chr9:139743496-139744228	K562	blood:	n/a	n/a
8	TBP	chr9:139743248-139744089	HepG2	liver:	n/a	n/a
9	TEAD4	chr9:139743437-139744383	K562	blood:	n/a	n/a
10	POLR2A	chr9:139742054-139747031	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:139743474-139748149	GM12892	blood:	n/a	n/a
12	POLR2A	chr9:139743017-139744818	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr9:139743446-139744306	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr9:139743099-139744194	GM19099	blood:	n/a	n/a
15	POLR2A	chr9:139742913-139744217	GM18526	blood:	n/a	n/a
16	BCL3	chr9:139743350-139745622	A549	lung:	n/a	n/a
17	MEF2C	chr9:139743493-139744100	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:139743427-139745171	ECC-1	luminal epithelium:	n/a	n/a
19	POU2F2	chr9:139743474-139744118	GM12878	blood:	n/a	n/a
20	POU2F2	chr9:139743446-139744099	GM12891	blood:	n/a	n/a
21	POLR2A	chr9:139741410-139744972	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr9:139743219-139744115	HepG2	liver:	n/a	n/a
23	POLR2A	chr9:139743454-139744109	GM12891	blood:	n/a	n/a
24	PML	chr9:139742990-139744643	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:139743417-139744107	HepG2	liver:	n/a	n/a
26	SP1	chr9:139743447-139744220	H1-hESC	embryonic stem cell:	n/a	chr9:139743815-139743826 chr9:139743855-139743866 chr9:139743871-139743882
27	POLR2A	chr9:139742050-139744427	K562	blood:	n/a	n/a
28	POLR2A	chr9:139743451-139744105	GM12892	blood:	n/a	n/a
29	POLR2A	chr9:139742122-139744337	GM18505	blood:	n/a	n/a
30	USF1	chr9:139743494-139744030	K562	blood:	n/a	n/a
31	E2F4	chr9:139743348-139744464	K562	blood:	n/a	n/a
32	SRF	chr9:139743494-139744156	ECC-1	luminal epithelium:	n/a	n/a
33	HEY1	chr9:139743447-139744100	HepG2	liver:	n/a	n/a
34	BRCA1	chr9:139743046-139744442	Hela-S3	cervix:	n/a	n/a
35	MAX	chr9:139741941-139744818	A549	lung:	n/a	chr9:139742492-139742501
36	EP300	chr9:139743378-139744100	A549	lung:	n/a	n/a
37	PML	chr9:139743428-139744847	MCF-7	breast:	n/a	n/a
38	BCL3	chr9:139743428-139744212	GM12878	blood:	n/a	n/a
39	POLR2A	chr9:139743472-139745144	H1-hESC	embryonic stem cell:	n/a	n/a
40	CEBPB	chr9:139743449-139744043	A549	lung:	n/a	chr9:139743637-139743648
41	ATF2	chr9:139743450-139744115	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr9:139743437-139744557	HCT-116	colon:	n/a	n/a
43	POLR2A	chr9:139740746-139744112	Hela-S3	cervix:	n/a	n/a
44	SP4	chr9:139743493-139744128	H1-hESC	embryonic stem cell:	n/a	chr9:139743815-139743826 chr9:139743855-139743866 chr9:139743871-139743882
45	CEBPB	chr9:139743241-139744303	Hela-S3	cervix:	n/a	chr9:139743637-139743648
46	MYBL2	chr9:139743436-139744120	HepG2	liver:	n/a	n/a
47	ZBTB7A	chr9:139741506-139743803	ECC-1	luminal epithelium:	n/a	n/a
48	TAF1	chr9:139742152-139744138	ECC-1	luminal epithelium:	n/a	n/a
49	JUN	chr9:139741920-139744807	K562	blood:	n/a	chr9:139742336-139742345 chr9:139742341-139742350 chr9:139742145-139742154
50	NFATC1	chr9:139743459-139744194	GM12878	blood:	n/a	n/a

No data

(count:52 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr9:139701264..139705082-chr9:139739803..139744148,9	K562	blood:
2	chr9:139619294..139624280-chr9:139740511..139747015,10	K562	blood:
3	chr9:139684658..139687578-chr9:139740553..139743920,5	K562	blood:
4	chr9:139742375..139744836-chr9:139963884..139966803,2	MCF-7	breast:
5	chr9:139734155..139746957-chr9:139834710..139842618,30	MCF-7	breast:
6	chr9:139742324..139745223-chr9:139913361..139916177,2	K562	blood:
7	chr9:139741064..139745722-chr9:139927339..139931121,5	MCF-7	breast:
8	chr9:139741779..139744858-chr9:139831668..139834703,3	MCF-7	breast:
9	chr9:139742045..139743770-chr9:139827741..139830305,2	MCF-7	breast:
10	chr9:139743062..139745588-chr9:139889291..139892478,4	MCF-7	breast:
11	chr9:139742204..139744989-chr9:139922690..139924315,2	K562	blood:
12	chr9:139742400..139745338-chr9:139946860..139949492,4	MCF-7	breast:
13	chr9:139741905..139746962-chr9:139835280..139841074,9	K562	blood:
14	chr9:139742958..139743712-chr9:139780306..139780835,2	Hela-S3	cervix:
15	chr9:139740484..139744006-chr9:140134528..140138502,3	MCF-7	breast:
16	chr9:139620371..139624237-chr9:139739421..139743672,6	K562	blood:
17	chr9:139742018..139745799-chr9:139919538..139925328,8	MCF-7	breast:
18	chr9:139739695..139750977-chr9:139884187..139892196,24	MCF-7	breast:
19	chr9:139684238..139687578-chr9:139742280..139744165,4	K562	blood:
20	chr11:65480015..65480549-chr9:139743272..139744189,2	NB4	blood:
21	chr9:139742261..139744866-chr9:139815519..139817769,2	MCF-7	breast:
22	chr9:139739152..139745418-chr9:139778222..139783565,14	K562	blood:
23	chr9:139741905..139745759-chr9:139836394..139841074,11	K562	blood:
24	chr9:139622227..139624694-chr9:139741896..139744177,2	MCF-7	breast:
25	chr9:139708650..139712209-chr9:139740733..139743918,4	K562	blood:
26	chr9:139741392..139743891-chr9:139890896..139894432,4	K562	blood:
27	chr9:139740288..139765167-chr9:139774067..139789146,84	MCF-7	breast:
28	chr9:139741638..139745300-chr9:139796064..139800031,7	MCF-7	breast:
29	chr9:139742078..139744191-chr9:139885946..139887958,2	K562	blood:
30	chr9:139682478..139689029-chr9:139739017..139745111,14	MCF-7	breast:
31	chr9:139719747..139722199-chr9:139741571..139743899,3	MCF-7	breast:
32	chr17:57913548..57915652-chr9:139742482..139745251,2	MCF-7	breast:
33	chr9:139739931..139767051-chr9:139773561..139787082,72	MCF-7	breast:
34	chr9:139741435..139745914-chr9:139791926..139799555,14	MCF-7	breast:
35	chr9:139742573..139744180-chr9:140135641..140137382,2	K562	blood:
36	chr9:139740616..139744257-chr9:139921749..139926263,5	MCF-7	breast:
37	chr9:139692582..139697157-chr9:139741560..139746001,12	MCF-7	breast:
38	chr9:139708902..139712209-chr9:139739346..139743918,5	K562	blood:
39	chr9:139742564..139744114-chr9:139842941..139845499,2	K562	blood:
40	chr9:139701264..139707085-chr9:139739803..139744391,11	K562	blood:
41	chr9:139742926..139745280-chr9:139887181..139889279,2	MCF-7	breast:
42	chr9:139741649..139744546-chr9:139793332..139795839,3	MCF-7	breast:
43	chr9:139741884..139743712-chr9:139842627..139845556,4	MCF-7	breast:
44	chr9:139697895..139704462-chr9:139739339..139746143,17	MCF-7	breast:
45	chr9:139606186..139609048-chr9:139741254..139743586,2	MCF-7	breast:
46	chr9:139682195..139706361-chr9:139728316..139752024,110	MCF-7	breast:
47	chr9:139738593..139754524-chr9:139832961..139844322,29	MCF-7	breast:
48	chr9:139740102..139743875-chr9:139939807..139943151,4	MCF-7	breast:
49	chr9:139741127..139744011-chr9:140062482..140064332,2	MCF-7	breast:
50	chr9:139740736..139746036-chr9:139779239..139783690,13	K562	blood:

No data

Variant related genes	Relation type
PHPT1	TF binding region
MAMDC4	TF binding region
ENSG00000186193	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000213590	Chromatin interaction
ENSG00000176919	Chromatin interaction
ENSG00000273066	Chromatin interaction
ENSG00000196642	Chromatin interaction
ENSG00000228544	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000236394	Chromatin interaction
ENSG00000213213	Chromatin interaction
ENSG00000184925	Chromatin interaction
ENSG00000165716	Chromatin interaction
ENSG00000263697	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000180539	Chromatin interaction
ENSG00000107331	Chromatin interaction
ENSG00000244187	Chromatin interaction
ENSG00000260190	Chromatin interaction
ENSG00000272679	Chromatin interaction
ENSG00000127191	Chromatin interaction
ENSG00000180549	Chromatin interaction
ENSG00000272896	Chromatin interaction
ENSG00000233016	Chromatin interaction
ENSG00000159069	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000213212	Chromatin interaction
ENSG00000107281	Chromatin interaction
ENSG00000266507	Chromatin interaction
ENSG00000054179	Chromatin interaction
ENSG00000169583	Chromatin interaction
ENSG00000148362	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10123375	0.82[JPT][hapmap]
rs10747037	0.82[JPT][hapmap]
rs10781520	0.82[JPT][hapmap]
rs10781524	0.82[JPT][hapmap]
rs10870140	0.82[JPT][hapmap]
rs13301872	1.00[JPT][hapmap]
rs1800631	0.82[JPT][hapmap]
rs2077581	0.82[JPT][hapmap]
rs2386139	0.82[JPT][hapmap]
rs2386140	0.82[JPT][hapmap]
rs2784074	0.82[JPT][hapmap]
rs2784075	1.00[JPT][hapmap]
rs2784080	0.82[JPT][hapmap]
rs2784081	0.82[JPT][hapmap]
rs2784088	0.82[JPT][hapmap]
rs2811757	0.82[JPT][hapmap]
rs2811758	0.82[JPT][hapmap]
rs2811761	0.82[JPT][hapmap]
rs2811762	0.82[JPT][hapmap]
rs3739942	0.82[JPT][hapmap]
rs3739943	0.82[JPT][hapmap]
rs3750511	0.82[JPT][hapmap]
rs3750512	0.82[JPT][hapmap]
rs4636298	0.82[JPT][hapmap]
rs4880076	0.82[JPT][hapmap]
rs4880153	0.82[JPT][hapmap]
rs4880157	0.82[JPT][hapmap]
rs4880158	0.82[JPT][hapmap]
rs4880160	0.82[JPT][hapmap]
rs4880162	0.82[JPT][hapmap]
rs4880163	0.82[JPT][hapmap]
rs4880166	0.82[JPT][hapmap]
rs4880168	0.82[JPT][hapmap]
rs7027246	0.82[JPT][hapmap]
rs7028946	0.82[JPT][hapmap]
rs7047374	0.82[JPT][hapmap]
rs7048473	0.82[JPT][hapmap]
rs7868124	0.82[JPT][hapmap]
rs7868660	0.82[JPT][hapmap]
rs7869864	0.82[JPT][hapmap]
rs872463	0.82[JPT][hapmap]
rs908831	0.82[JPT][hapmap]
rs945385	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:70 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1849811	chr9:138939662-139755001	Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	323 gene(s)	inside rSNPs	diseases
2	esv1822553	chr9:138967205-139755539	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	323 gene(s)	inside rSNPs	diseases
3	nsv430118	chr9:139101947-139795504	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	299 gene(s)	inside rSNPs	diseases
4	nsv540342	chr9:139218422-139973312	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	317 gene(s)	inside rSNPs	diseases
5	esv2758204	chr9:139252829-139826485	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	270 gene(s)	inside rSNPs	diseases
6	esv2759720	chr9:139252829-139826485	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	270 gene(s)	inside rSNPs	diseases
7	nsv469918	chr9:139254317-140068342	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	341 gene(s)	inside rSNPs	diseases
8	nsv540346	chr9:139360142-140164011	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	471 gene(s)	inside rSNPs	diseases
9	nsv1039149	chr9:139376829-139991102	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	303 gene(s)	inside rSNPs	diseases
10	esv1829857	chr9:139385438-139760041	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
11	esv1819204	chr9:139388365-139758238	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
12	esv1803979	chr9:139395473-139979276	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	267 gene(s)	inside rSNPs	diseases
13	esv1831778	chr9:139395473-139979276	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	267 gene(s)	inside rSNPs	diseases
14	esv1821575	chr9:139395473-140068342	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
15	esv2422220	chr9:139478587-140244550	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	454 gene(s)	inside rSNPs	diseases
16	nsv894409	chr9:139483954-139860264	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	209 gene(s)	inside rSNPs	diseases
17	nsv894422	chr9:139487092-139776400	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
18	nsv894432	chr9:139522101-139869914	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	205 gene(s)	inside rSNPs	diseases
19	nsv894440	chr9:139544437-139841512	Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
20	nsv894441	chr9:139544437-139860264	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
21	nsv894442	chr9:139544437-140462099	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
22	nsv894450	chr9:139598108-139776400	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	130 gene(s)	inside rSNPs	diseases
23	nsv894451	chr9:139598108-139995065	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
24	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
25	nsv894454	chr9:139607966-139904037	Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	172 gene(s)	inside rSNPs	diseases
26	nsv894455	chr9:139607966-140411547	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	417 gene(s)	inside rSNPs	diseases
27	nsv818738	chr9:139634495-139904037	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	126 gene(s)	inside rSNPs	diseases
28	nsv894457	chr9:139650448-139776400	Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
29	nsv894458	chr9:139683224-139776400	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
30	nsv894459	chr9:139683224-139787453	Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
31	nsv894460	chr9:139683224-139810595	Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
32	nsv894461	chr9:139683224-139860264	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
33	nsv894462	chr9:139683224-140274164	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	353 gene(s)	inside rSNPs	diseases
34	nsv894463	chr9:139683224-140411547	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
35	esv29973	chr9:139690144-139754110	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
36	nsv894464	chr9:139690144-139776400	Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
37	nsv894465	chr9:139690144-139795504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	76 gene(s)	inside rSNPs	diseases
38	esv1846327	chr9:139690144-139841512	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	86 gene(s)	inside rSNPs	diseases
39	nsv524322	chr9:139690144-140376668	Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	371 gene(s)	inside rSNPs	diseases
40	nsv894466	chr9:139693992-139784683	Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
41	nsv894467	chr9:139693992-139810595	Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
42	nsv894468	chr9:139693992-139860264	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
43	nsv894469	chr9:139693992-140118448	Bivalent Enhancer Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
44	nsv894470	chr9:139693992-140339091	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	358 gene(s)	inside rSNPs	diseases
45	nsv894471	chr9:139694521-139776400	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases
46	nsv894472	chr9:139694521-139787453	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
47	nsv894473	chr9:139694521-139810595	Bivalent/Poised TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
48	nsv894474	chr9:139694521-140432318	Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
49	nsv894475	chr9:139694569-139786465	Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
50	nsv540352	chr9:139695108-140351178	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	358 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12555238	EDF1	Cis_1M	lymphoblastoid	RTeQTL
rs12555238	NDOR1	cis	parietal	SCAN
rs12555238	PHPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:139740600-139744200	Active TSS	Hela-S3	cervix
2	chr9:139740800-139744800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:139741000-139744600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr9:139741000-139744800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr9:139741200-139744400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:139741200-139744400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:139741200-139744400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:139741200-139744400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:139741200-139744600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr9:139741400-139744400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:139741400-139744600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:139741400-139744800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr9:139741400-139744800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:139741600-139744400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:139741600-139744400	Active TSS	Psoas Muscle	Psoas
16	chr9:139741600-139744800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr9:139741800-139743800	Active TSS	Right Atrium	heart
18	chr9:139741800-139744200	Active TSS	Esophagus	oesophagus
19	chr9:139741800-139744400	Active TSS	Left Ventricle	heart
20	chr9:139741800-139744600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:139742000-139744200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:139742000-139744200	Active TSS	GM12878-XiMat	blood
23	chr9:139742000-139744400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:139742000-139744400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr9:139742000-139744600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:139742000-139744600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:139742000-139744600	Active TSS	HSMM	muscle
28	chr9:139742000-139744600	Active TSS	HSMMtube	muscle
29	chr9:139742000-139745000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr9:139742200-139744200	Active TSS	Fetal Intestine Large	intestine
31	chr9:139742200-139744200	Active TSS	Pancreas	Pancrea
32	chr9:139742200-139744400	Active TSS	Small Intestine	intestine
33	chr9:139742200-139744600	Active TSS	Placenta Amnion	Placenta Amnion
34	chr9:139742200-139744600	Active TSS	A549	lung
35	chr9:139742200-139745000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr9:139742400-139744400	Active TSS	Fetal Heart	heart
37	chr9:139742400-139744400	Active TSS	NHDF-Ad	bronchial
38	chr9:139742400-139744600	Active TSS	K562	blood
39	chr9:139742400-139744800	Active TSS	Fetal Kidney	kidney
40	chr9:139742600-139743600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr9:139742600-139744200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:139742600-139744200	Active TSS	Right Ventricle	heart
43	chr9:139742600-139744400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:139742600-139744400	Active TSS	Gastric	stomach
45	chr9:139742600-139744600	Active TSS	Aorta	Aorta
46	chr9:139742800-139743600	Enhancers	Fetal Brain Male	brain
47	chr9:139742800-139743600	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr9:139742800-139744000	Active TSS	Stomach Mucosa	stomach
49	chr9:139742800-139744200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr9:139742800-139744200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links