Variant report

Variant	rs58952707
Chromosome Location	chr9:71784166-71784167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:71784054-71784193	HepG2	liver:	n/a	n/a
2	EP300	chr9:71783972-71784200	K562	blood:	n/a	n/a
3	ZNF384	chr9:71783561-71784314	K562	blood:	n/a	n/a
4	IRF4	chr9:71783726-71784245	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:71783737-71784278	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr9:71783895-71784176	H1-hESC	embryonic stem cell:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
7	SMC3	chr9:71783894-71784191	HepG2	liver:	n/a	n/a
8	CEBPB	chr9:71783886-71784228	Hela-S3	cervix:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
9	MYC	chr9:71783780-71784246	MCF10A-Er-Src	breast:	n/a	chr9:71783946-71783956
10	KAP1	chr9:71783870-71784257	U2OS	brain:	n/a	n/a
11	RFX5	chr9:71783905-71784171	HepG2	liver:	n/a	n/a
12	FOS	chr9:71783780-71784235	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr9:71783753-71784271	MCF10A-Er-Src	breast:	n/a	chr9:71783760-71783771 chr9:71784050-71784058
14	CEBPB	chr9:71783780-71784226	MCF-7	breast:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
15	FOS	chr9:71783783-71784244	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr9:71783843-71784214	K562	blood:	n/a	chr9:71784020-71784035 chr9:71784024-71784035 chr9:71784021-71784031 chr9:71784015-71784035 chr9:71784025-71784036 chr9:71784025-71784036 chr9:71784017-71784033 chr9:71784018-71784032 chr9:71784024-71784035
17	HDAC2	chr9:71783832-71784276	MCF-7	breast:	n/a	n/a
18	MAFF	chr9:71783826-71784223	HepG2	liver:	n/a	chr9:71784018-71784032 chr9:71784019-71784037
19	CEBPD	chr9:71783950-71784178	HepG2	liver:	n/a	chr9:71784048-71784059 chr9:71784047-71784058
20	MAFK	chr9:71783897-71784171	Hela-S3	cervix:	n/a	chr9:71784020-71784035 chr9:71784024-71784035 chr9:71784021-71784031 chr9:71784015-71784035 chr9:71784025-71784036 chr9:71784025-71784036 chr9:71784017-71784033 chr9:71784018-71784032 chr9:71784024-71784035
21	BATF	chr9:71783680-71784242	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr9:71783745-71784307	MCF-7	breast:	n/a	n/a
23	ATF2	chr9:71783777-71784242	GM12878	blood:	n/a	n/a
24	MAFK	chr9:71783829-71784214	HepG2	liver:	n/a	chr9:71784020-71784035 chr9:71784024-71784035 chr9:71784021-71784031 chr9:71784015-71784035 chr9:71784025-71784036 chr9:71784025-71784036 chr9:71784017-71784033 chr9:71784018-71784032 chr9:71784024-71784035
25	CEBPB	chr9:71783867-71784243	K562	blood:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
26	CEBPB	chr9:71783868-71784233	HepG2	liver:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
27	ATF2	chr9:71783919-71784211	GM12878	blood:	n/a	n/a
28	FOXA1	chr9:71783793-71784197	HepG2	liver:	n/a	n/a
29	JUND	chr9:71783802-71784213	K562	blood:	n/a	n/a
30	RCOR1	chr9:71783776-71784179	K562	blood:	n/a	n/a
31	CEBPB	chr9:71783860-71784251	IMR90	lung:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
32	STAT3	chr9:71783751-71784199	MCF10A-Er-Src	breast:	n/a	chr9:71783760-71783771 chr9:71784050-71784058
33	CEBPB	chr9:71783753-71784362	MCF-7	breast:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
34	FOXA2	chr9:71783855-71784240	HepG2	liver:	n/a	n/a
35	BATF	chr9:71783851-71784225	GM12878	blood:	n/a	n/a
36	FOXA1	chr9:71783838-71784301	HepG2	liver:	n/a	n/a
37	NFIC	chr9:71783556-71784262	GM12878	blood:	n/a	n/a
38	STAT3	chr9:71783763-71784214	MCF10A-Er-Src	breast:	n/a	chr9:71784050-71784058
39	ZNF384	chr9:71783525-71784274	GM12878	blood:	n/a	n/a
40	MAFK	chr9:71783833-71784220	H1-hESC	embryonic stem cell:	n/a	chr9:71784020-71784035 chr9:71784024-71784035 chr9:71784021-71784031 chr9:71784015-71784035 chr9:71784025-71784036 chr9:71784025-71784036 chr9:71784017-71784033 chr9:71784018-71784032 chr9:71784024-71784035
41	TBL1XR1	chr9:71783710-71784177	GM12878	blood:	n/a	n/a
42	MTA3	chr9:71783578-71784210	GM12878	blood:	n/a	n/a
43	CEBPB	chr9:71783873-71784255	HepG2	liver:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
44	BHLHE40	chr9:71783678-71784198	GM12878	blood:	n/a	n/a
45	CEBPB	chr9:71783886-71784232	K562	blood:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
46	FOS	chr9:71783840-71784223	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr9:71783764-71784214	MCF10A-Er-Src	breast:	n/a	chr9:71784050-71784058
48	CEBPB	chr9:71783947-71784182	A549	lung:	n/a	chr9:71784047-71784058 chr9:71784048-71784059
49	FOXA1	chr9:71783799-71784234	HepG2	liver:	n/a	n/a
50	MYC	chr9:71783780-71784215	MCF10A-Er-Src	breast:	n/a	chr9:71783946-71783956

No.	Distal block	Cell Line	Cell type
1	chr9:71782411..71787293-chr9:71788939..71792215,6	K562	blood:
2	chr9:71782838..71785289-chr9:71817558..71819101,2	MCF-7	breast:
3	chr9:71735183..71737374-chr9:71783911..71785475,2	MCF-7	breast:
4	chr9:71735247..71737414-chr9:71784064..71786040,3	MCF-7	breast:
5	chr9:71783839..71786700-chr9:71787846..71790491,3	MCF-7	breast:
6	chr9:71779511..71782336-chr9:71782342..71784212,2	MCF-7	breast:

Variant related genes	Relation type
TJP2	TF binding region
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs57260043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57364596	1.00[EUR][1000 genomes]
rs57847527	0.88[AFR][1000 genomes]
rs58812039	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60225159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60717517	0.94[AFR][1000 genomes]
rs73449168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73449175	1.00[AMR][1000 genomes]
rs73450836	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
21	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71752000-71788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:71755600-71788600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:71765000-71787800	Weak transcription	Left Ventricle	heart
4	chr9:71765000-71788600	Weak transcription	Gastric	stomach
5	chr9:71767600-71787800	Weak transcription	Fetal Heart	heart
6	chr9:71767600-71787800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:71769000-71788000	Weak transcription	Fetal Kidney	kidney
8	chr9:71769400-71785000	Weak transcription	HUVEC	blood vessel
9	chr9:71770600-71788600	Weak transcription	Esophagus	oesophagus
10	chr9:71770800-71788400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:71770800-71788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:71776200-71785600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:71776200-71788000	Weak transcription	Pancreas	Pancrea
14	chr9:71777400-71788400	Weak transcription	Right Atrium	heart
15	chr9:71779400-71785400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:71779600-71788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:71779800-71785400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:71780800-71787800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:71781000-71787800	Weak transcription	Fetal Stomach	stomach
20	chr9:71781400-71785400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:71781400-71788600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:71781600-71787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:71782000-71787800	Weak transcription	Fetal Intestine Small	intestine
24	chr9:71782800-71784200	Enhancers	HepG2	liver
25	chr9:71783000-71784200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:71783000-71785400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:71783000-71785400	Enhancers	NHEK	skin
28	chr9:71783200-71784200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:71783200-71784200	Enhancers	Fetal Intestine Large	intestine
30	chr9:71783200-71784200	Enhancers	Small Intestine	intestine
31	chr9:71783200-71784400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr9:71783200-71785600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:71783400-71784200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr9:71783400-71784200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr9:71783600-71784200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:71783600-71784200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr9:71783600-71784200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr9:71783600-71784200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr9:71783600-71784200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr9:71783600-71784200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:71783600-71784200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr9:71783600-71785800	Enhancers	HMEC	breast
43	chr9:71783600-71785800	Enhancers	K562	blood
44	chr9:71783800-71784200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr9:71783800-71784200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr9:71783800-71784200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr9:71783800-71784200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr9:71783800-71784200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr9:71783800-71784200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:71783800-71784200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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