Variant report

Variant	rs6932738
Chromosome Location	chr6:56200590-56200591
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	SP1	chr6:56200418-56201041	HCT-116	colon:	n/a	n/a
2	GATA3	chr6:56199487-56201096	SK-N-SH	brain:	n/a	n/a
3	CHD2	chr6:56200518-56200939	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr6:56200590-56200910	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr6:56200427-56201033	HCT-116	colon:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
6	ATF3	chr6:56200502-56201043	HCT-116	colon:	n/a	n/a
7	ATF3	chr6:56200558-56201056	HCT-116	colon:	n/a	n/a
8	EP300	chr6:56200526-56200946	SK-N-SH_RA	brain:	n/a	n/a
9	NFIC	chr6:56200352-56201101	SK-N-SH	brain:	n/a	n/a
10	USF2	chr6:56200326-56201149	Hela-S3	cervix:	n/a	n/a
11	FOS	chr6:56200536-56200959	Hela-S3	cervix:	n/a	chr6:56200736-56200747 chr6:56200779-56200789 chr6:56200779-56200789 chr6:56200778-56200789
12	JUN	chr6:56200577-56200973	HUVEC	blood vessel:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
13	RFX5	chr6:56199733-56201031	Hela-S3	cervix:	n/a	n/a
14	PBX3	chr6:56200520-56201038	SK-N-SH	brain:	n/a	n/a
15	EP300	chr6:56200374-56201027	SK-N-SH	brain:	n/a	n/a
16	FOSL1	chr6:56200442-56201136	HCT-116	colon:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
17	EP300	chr6:56200504-56200987	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr6:56200439-56201001	SK-N-SH	brain:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
19	SRF	chr6:56200430-56201095	HCT-116	colon:	n/a	n/a
20	RCOR1	chr6:56200514-56200968	Hela-S3	cervix:	n/a	n/a
21	TCF12	chr6:56199584-56201124	SK-N-SH	brain:	n/a	n/a
22	PBX3	chr6:56200496-56200987	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr6:56200451-56200950	HCT-116	colon:	n/a	n/a
24	FOSL2	chr6:56200567-56200919	A549	lung:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
25	CEBPB	chr6:56200564-56200993	IMR90	lung:	n/a	n/a
26	BRCA1	chr6:56200541-56200997	Hela-S3	cervix:	n/a	n/a
27	MEF2A	chr6:56199653-56200970	SK-N-SH	brain:	n/a	n/a
28	TEAD4	chr6:56200446-56201039	SK-N-SH	brain:	n/a	n/a
29	FOS	chr6:56200514-56200992	MCF10A-Er-Src	breast:	n/a	chr6:56200736-56200747 chr6:56200779-56200789 chr6:56200779-56200789 chr6:56200778-56200789
30	POLR2A	chr6:56199793-56201077	IMR90	lung:	n/a	n/a
31	CEBPB	chr6:56200406-56201148	HCT-116	colon:	n/a	n/a
32	JUND	chr6:56200382-56201033	SK-N-SH	brain:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
33	POLR2A	chr6:56200547-56200896	Hela-S3	cervix:	n/a	n/a
34	FOS	chr6:56200552-56200997	MCF10A-Er-Src	breast:	n/a	chr6:56200736-56200747 chr6:56200779-56200789 chr6:56200779-56200789 chr6:56200778-56200789
35	FOSL2	chr6:56200512-56201022	SK-N-SH	brain:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
36	JUND	chr6:56200404-56201099	SK-N-SH	brain:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
37	TEAD4	chr6:56200448-56201060	SK-N-SH	brain:	n/a	n/a
38	SP1	chr6:56200445-56201006	HCT-116	colon:	n/a	n/a
39	MYC	chr6:56200585-56200937	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr6:56200508-56200923	SK-N-SH	brain:	n/a	n/a
41	CEBPB	chr6:56200488-56201058	A549	lung:	n/a	n/a
42	FOS	chr6:56200535-56200976	HUVEC	blood vessel:	n/a	chr6:56200736-56200747 chr6:56200779-56200789 chr6:56200779-56200789 chr6:56200778-56200789
43	POLR2A	chr6:56200488-56200941	U87	brain:	n/a	n/a
44	MAFK	chr6:56200501-56200954	IMR90	lung:	n/a	n/a
45	POLR2A	chr6:56200397-56200941	U87	brain:	n/a	n/a
46	TCF12	chr6:56199513-56201131	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr6:56199530-56201131	SK-N-SH	brain:	n/a	n/a
48	FOSL2	chr6:56200504-56200977	A549	lung:	n/a	chr6:56200779-56200789 chr6:56200779-56200789
49	ZKSCAN1	chr6:56199746-56201000	Hela-S3	cervix:	n/a	n/a
50	FOS	chr6:56200531-56201027	MCF10A-Er-Src	breast:	n/a	chr6:56200736-56200747 chr6:56200779-56200789 chr6:56200779-56200789 chr6:56200778-56200789

Variant related genes	Relation type
ENSG00000227602	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10456731	0.88[CHB][hapmap]
rs13205765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2397216	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397217	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397219	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2894835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629685	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459151	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459152	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6459153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901838	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6907967	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909274	0.83[EUR][1000 genomes]
rs6911570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924804	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357911	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370522	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475663	0.80[CEU][hapmap]
rs9475664	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9475665	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9475666	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9475669	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9475671	0.85[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56194400-56203600	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:56199000-56201400	Enhancers	NHDF-Ad	bronchial
3	chr6:56199000-56201400	Enhancers	NHEK	skin
4	chr6:56199000-56201800	Enhancers	HMEC	breast
5	chr6:56199200-56201000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:56199200-56201000	Enhancers	Osteobl	bone
7	chr6:56199200-56201400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:56199200-56201400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:56199400-56200800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:56199400-56200800	Enhancers	HSMM	muscle
11	chr6:56199400-56201000	Enhancers	HUVEC	blood vessel
12	chr6:56199400-56201000	Enhancers	NHLF	lung
13	chr6:56199400-56201200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:56199400-56201800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:56199600-56201200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:56199600-56202400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:56200000-56200600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:56200000-56200600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr6:56200000-56201000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:56200200-56200600	Enhancers	A549	lung
21	chr6:56200200-56200600	Flanking Active TSS	Hela-S3	cervix
22	chr6:56200200-56200600	Flanking Active TSS	NH-A	brain
23	chr6:56200200-56201000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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