Variant report

Variant	rs11961041
Chromosome Location	chr6:34709909-34709910
allele	A/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	FOXA1	chr6:34709743-34710295	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:34709841-34710316	HepG2	liver:	n/a	n/a
3	STAT3	chr6:34709871-34710261	MCF10A-Er-Src	breast:	n/a	chr6:34710091-34710102
4	ARID3A	chr6:34709883-34710222	HepG2	liver:	n/a	n/a
5	FOXA1	chr6:34709865-34710197	HepG2	liver:	n/a	n/a
6	STAT3	chr6:34709873-34710311	MCF10A-Er-Src	breast:	n/a	chr6:34710091-34710102
7	FOS	chr6:34709850-34710250	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA2	chr6:34709873-34710176	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000217130	TF binding region

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1018622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1051115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11963234	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11966100	0.89[EUR][1000 genomes]
rs11967912	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11968954	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11968972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1201872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12111129	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13193526	0.80[ASN][1000 genomes]
rs13195029	0.85[EUR][1000 genomes]
rs13195361	0.89[EUR][1000 genomes]
rs13195490	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs13196983	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13200792	0.85[EUR][1000 genomes]
rs13205210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs13206245	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208149	0.89[EUR][1000 genomes]
rs13209544	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13210470	0.89[EUR][1000 genomes]
rs13212699	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13213239	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13213288	0.89[EUR][1000 genomes]
rs13213604	0.89[EUR][1000 genomes]
rs13214596	0.92[EUR][1000 genomes]
rs16892386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16895659	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs205261	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs205262	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs205263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs205265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs205266	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs205267	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs205284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2296361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs2296362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs2395603	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395605	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28360525	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34261333	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34355573	0.89[EUR][1000 genomes]
rs34377413	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34463942	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34480956	0.89[EUR][1000 genomes]
rs34681295	0.92[EUR][1000 genomes]
rs34840245	0.89[EUR][1000 genomes]
rs35081279	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35103554	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35143960	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35186650	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35195182	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35203657	0.89[EUR][1000 genomes]
rs35285054	0.80[ASN][1000 genomes]
rs35369977	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35444671	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35684630	0.83[ASN][1000 genomes]
rs35744142	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940001	0.89[EUR][1000 genomes]
rs36026951	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3734266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4438945	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs451263	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs451603	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4646933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6457792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6457796	0.85[CHB][hapmap]
rs6457797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6457798	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66672772	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66926909	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67622212	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67895864	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6900426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6904996	0.88[EUR][1000 genomes]
rs6908462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909393	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6910824	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6914031	0.80[EUR][1000 genomes]
rs6914351	0.86[EUR][1000 genomes]
rs6925175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6926373	0.89[EUR][1000 genomes]
rs6934741	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71567467	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72892238	0.94[ASN][1000 genomes]
rs72892286	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72910111	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72910167	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7743724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs7749750	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755354	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7758743	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759412	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759985	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761391	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7763989	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7764126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7764921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7775947	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776439	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912717	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9461992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9462001	0.88[ASN][1000 genomes]
rs9462002	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462003	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469812	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9469813	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9469847	0.86[ASN][1000 genomes]
rs9469852	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9968782	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers 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 target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 target site	42 gene(s)	inside rSNPs	diseases
12	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv508401	chr6:34669708-34710302	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv885795	chr6:34704613-34823187	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv965713	chr6:34708188-34713851	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11961041	UHRF1BP1	cis	Muscle Skeletal	GTEx
rs11961041	C6orf107	cis	uninvolved skin	skin_eQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34698000-34714000	Weak transcription	Esophagus	oesophagus
2	chr6:34699800-34712200	Weak transcription	Stomach Mucosa	stomach
3	chr6:34706400-34712800	Enhancers	HepG2	liver
4	chr6:34708400-34712800	Weak transcription	A549	lung
5	chr6:34708600-34711200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:34708600-34712200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:34708600-34712200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:34708600-34712600	Weak transcription	Hela-S3	cervix
9	chr6:34708600-34713000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:34708600-34713200	Weak transcription	Liver	Liver
11	chr6:34708800-34711400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:34709000-34711200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:34709000-34711200	Weak transcription	NHEK	skin
14	chr6:34709000-34711600	Weak transcription	Fetal Intestine Large	intestine
15	chr6:34709000-34712800	Weak transcription	K562	blood
16	chr6:34709400-34712200	Weak transcription	Small Intestine	intestine

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