Variant report

Variant	rs669838
Chromosome Location	chr18:11994598-11994599
allele	G/T
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	chr18:11994502-11995667	HepG2	liver:	n/a	n/a
2	CHD2	chr18:11994511-11994804	HepG2	liver:	n/a	n/a
3	FOS	chr18:11994339-11995025	MCF10A-Er-Src	breast:	n/a	chr18:11994939-11994946 chr18:11994938-11994946 chr18:11994937-11994947 chr18:11994938-11994946
4	MAX	chr18:11994341-11995703	Hela-S3	cervix:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
5	FOXA2	chr18:11994318-11994707	HepG2	liver:	n/a	n/a
6	TBP	chr18:11994520-11994999	HepG2	liver:	n/a	n/a
7	MAZ	chr18:11994217-11996003	IMR90	lung:	n/a	chr18:11994937-11994946
8	MXI1	chr18:11994401-11995255	HepG2	liver:	n/a	n/a
9	CEBPB	chr18:11994290-11994925	HepG2	liver:	n/a	chr18:11994620-11994633
10	FOXA1	chr18:11994273-11994807	HepG2	liver:	n/a	n/a
11	ZKSCAN1	chr18:11994323-11994655	Hela-S3	cervix:	n/a	n/a
12	MAX	chr18:11994311-11995863	HepG2	liver:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
13	SMC3	chr18:11994455-11995935	HepG2	liver:	n/a	n/a
14	TEAD4	chr18:11994223-11994825	HepG2	liver:	n/a	n/a
15	MAX	chr18:11994248-11995839	A549	lung:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
16	POLR2A	chr18:11994227-11996555	HL-60	blood:	n/a	n/a
17	CEBPB	chr18:11994309-11994708	HepG2	liver:	n/a	chr18:11994620-11994633
18	TCF12	chr18:11994151-11995669	A549	lung:	n/a	n/a
19	POLR2A	chr18:11993291-11997275	Hela-S3	cervix:	n/a	n/a
20	EP300	chr18:11994335-11994733	Hela-S3	cervix:	n/a	chr18:11994621-11994635
21	POLR2A	chr18:11994264-11995704	Hela-S3	cervix:	n/a	n/a
22	STAT3	chr18:11994309-11994650	MCF10A-Er-Src	breast:	n/a	chr18:11994412-11994420
23	RCOR1	chr18:11994397-11994685	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr18:11994498-11996051	K562	blood:	n/a	n/a
25	CTCF	chr18:11994560-11994710	HBMEC	blood vessel:	n/a	n/a
26	MYBL2	chr18:11994405-11995258	HepG2	liver:	n/a	n/a
27	RAD21	chr18:11994553-11995161	HepG2	liver:	n/a	n/a
28	FOS	chr18:11994311-11994647	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr18:11994308-11994898	HepG2	liver:	n/a	chr18:11994620-11994633
30	POLR2A	chr18:11994350-11994619	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr18:11994350-11994612	MCF10A-Er-Src	breast:	n/a	chr18:11994412-11994420
32	CEBPB	chr18:11994315-11994893	IMR90	lung:	n/a	chr18:11994620-11994633
33	TCF7L2	chr18:11994353-11994777	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr18:11994273-11994916	Hela-S3	cervix:	n/a	chr18:11994620-11994633
35	FOXA1	chr18:11994324-11994720	HepG2	liver:	n/a	n/a
36	STAT3	chr18:11994190-11994708	MCF10A-Er-Src	breast:	n/a	chr18:11994412-11994420
37	CEBPB	chr18:11994284-11994648	MCF-7	breast:	n/a	chr18:11994620-11994633
38	MAX	chr18:11994581-11995713	HepG2	liver:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
39	SMC3	chr18:11994259-11995797	Hela-S3	cervix:	n/a	n/a
40	TFAP2C	chr18:11994322-11994964	Hela-S3	cervix:	n/a	n/a
41	MAZ	chr18:11994346-11994997	Hela-S3	cervix:	n/a	chr18:11994937-11994946
42	POLR2A	chr18:11994160-11997305	HL-60	blood:	n/a	n/a
43	RFX5	chr18:11994316-11994760	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr18:11994178-11996104	HepG2	liver:	n/a	n/a
45	CHD2	chr18:11994328-11995023	Hela-S3	cervix:	n/a	n/a
46	EP300	chr18:11994366-11994784	HepG2	liver:	n/a	chr18:11994621-11994635
47	E2F4	chr18:11994353-11994664	MCF10A-Er-Src	breast:	n/a	n/a
48	SP1	chr18:11994250-11995191	A549	lung:	n/a	chr18:11995049-11995058 chr18:11995045-11995059 chr18:11995044-11995053
49	POLR2A	chr18:11994271-11995521	Hela-S3	cervix:	n/a	n/a
50	FOS	chr18:11994293-11994628	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:11994002..11996965-chr18:12008009..12011015,3	MCF-7	breast:
2	chr18:11992964..11995381-chr18:12038056..12040567,2	MCF-7	breast:
3	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:
4	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000141401	Chromatin interaction
ENSG00000266995	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs3859296	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs58393627	0.93[ASN][1000 genomes]
rs588257	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs589247	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs590100	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs590277	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591061	0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs592577	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604962	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs605047	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs605636	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs605964	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs606020	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606105	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606370	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606478	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs607200	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622061	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs622246	0.97[ASN][1000 genomes]
rs636173	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636300	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs638063	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs638125	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs644710	0.83[JPT][hapmap]
rs649396	0.95[ASN][1000 genomes]
rs649713	0.95[ASN][1000 genomes]
rs650727	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs655790	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs666521	0.96[ASN][1000 genomes]
rs667798	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs668223	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs671470	0.81[CEU][hapmap]
rs672917	0.81[CEU][hapmap]
rs682271	0.90[ASN][1000 genomes]
rs683190	0.90[ASN][1000 genomes]
rs684680	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7234493	0.81[CEU][hapmap]
rs9973072	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active 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
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-11995600	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
4	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
5	chr18:11984200-11994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:11984400-11995000	Weak transcription	GM12878-XiMat	blood
7	chr18:11986000-11995600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:11986400-11994600	Weak transcription	Liver	Liver
9	chr18:11987200-11994800	Weak transcription	Right Atrium	heart
10	chr18:11988000-11995600	Weak transcription	K562	blood
11	chr18:11988600-11995200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr18:11989400-11994600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr18:11989600-11996400	Enhancers	Pancreas	Pancrea
14	chr18:11989800-11994600	Weak transcription	Left Ventricle	heart
15	chr18:11990000-11994800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:11990200-11995200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr18:11990400-11994600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr18:11990400-11994600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:11990400-11994600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr18:11990600-11994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr18:11990600-11994600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:11990600-11995800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:11990800-11994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr18:11990800-11994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr18:11990800-11994600	Weak transcription	NHLF	lung
26	chr18:11990800-11994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:11990800-11994800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr18:11990800-11995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr18:11991000-11994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:11991000-11995200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr18:11991200-11994800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:11991400-11994600	Strong transcription	Fetal Stomach	stomach
34	chr18:11991600-11994600	Weak transcription	Psoas Muscle	Psoas
35	chr18:11991600-11994800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr18:11992000-11995000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr18:11992600-11995200	Weak transcription	Spleen	Spleen
38	chr18:11993200-11996600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:11993200-11996600	Enhancers	HSMMtube	muscle
40	chr18:11993200-11998000	Enhancers	Stomach Mucosa	stomach
41	chr18:11993200-11998400	Enhancers	Fetal Muscle Trunk	muscle
42	chr18:11993400-11994600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:11993400-11994800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:11993400-11995200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr18:11993400-11995800	Enhancers	Lung	lung
46	chr18:11993400-11996400	Enhancers	Placenta	Placenta
47	chr18:11993400-11999400	Enhancers	Fetal Muscle Leg	muscle
48	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr18:11993600-11995000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr18:11993600-11995000	Genic enhancers	Fetal Intestine Small	intestine

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