Variant report

Variant	rs7947978
Chromosome Location	chr11:67442043-67442044
allele	A/C
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	SIN3AK20	chr11:67441669-67443124	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr11:67441832-67442503	MCF-7	breast:	n/a	n/a
3	POLR2A	chr11:67441883-67442376	MCF-7	breast:	n/a	n/a
4	MYC	chr11:67441877-67442333	MCF10A-Er-Src	breast:	n/a	chr11:67442124-67442133
5	NR2F2	chr11:67441821-67442640	MCF-7	breast:	n/a	n/a
6	NFIC	chr11:67441913-67442579	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr11:67441914-67442205	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr11:67442027-67442454	T-47D	breast:	n/a	n/a
9	HDAC2	chr11:67441771-67442721	MCF-7	breast:	n/a	chr11:67442605-67442624
10	CEBPB	chr11:67441860-67442529	MCF-7	breast:	n/a	n/a
11	POLR2A	chr11:67441858-67442281	MCF-7	breast:	n/a	n/a
12	ZNF217	chr11:67441935-67442568	MCF-7	breast:	n/a	n/a
13	PML	chr11:67441894-67442504	MCF-7	breast:	n/a	n/a
14	EP300	chr11:67441896-67442540	MCF-7	breast:	n/a	n/a
15	SP1	chr11:67441942-67442630	HCT-116	colon:	n/a	chr11:67442218-67442229 chr11:67442219-67442233
16	MYC	chr11:67441985-67442367	MCF-7	breast:	n/a	chr11:67442124-67442133
17	SP1	chr11:67442025-67442382	H1-hESC	embryonic stem cell:	n/a	chr11:67442218-67442229 chr11:67442219-67442233
18	MAX	chr11:67442017-67442478	ECC-1	luminal epithelium:	n/a	chr11:67442124-67442133
19	TCF12	chr11:67441943-67442590	ECC-1	luminal epithelium:	n/a	chr11:67442574-67442581
20	EP300	chr11:67441893-67442622	MCF-7	breast:	n/a	n/a
21	NR2F2	chr11:67442018-67442630	MCF-7	breast:	n/a	n/a
22	FOS	chr11:67441985-67442216	MCF10A-Er-Src	breast:	n/a	n/a
23	HDAC2	chr11:67441951-67442567	MCF-7	breast:	n/a	n/a
24	ELF1	chr11:67441908-67442731	MCF-7	breast:	n/a	n/a
25	TCF12	chr11:67441877-67442654	ECC-1	luminal epithelium:	n/a	chr11:67442574-67442581
26	GATA3	chr11:67442032-67442521	MCF-7	breast:	n/a	n/a
27	FOXA1	chr11:67441971-67442394	T-47D	breast:	n/a	n/a
28	TEAD4	chr11:67441969-67442507	ECC-1	luminal epithelium:	n/a	n/a
29	EP300	chr11:67441998-67442509	ECC-1	luminal epithelium:	n/a	n/a
30	GATA3	chr11:67441880-67442881	MCF-7	breast:	n/a	n/a
31	GATA3	chr11:67441946-67442515	T-47D	breast:	n/a	n/a
32	ESR1	chr11:67442013-67442466	T-47D	breast:	n/a	n/a
33	GABPA	chr11:67441917-67442505	MCF-7	breast:	n/a	n/a
34	EP300	chr11:67441915-67442421	T-47D	breast:	n/a	n/a
35	MAX	chr11:67442006-67442526	ECC-1	luminal epithelium:	n/a	chr11:67442124-67442133
36	GATA3	chr11:67441868-67442613	MCF-7	breast:	n/a	n/a
37	MAX	chr11:67441766-67442646	MCF-7	breast:	n/a	chr11:67442124-67442133
38	EP300	chr11:67441906-67442532	T-47D	breast:	n/a	n/a
39	TCF12	chr11:67441668-67442759	MCF-7	breast:	n/a	chr11:67442574-67442581
40	GATA3	chr11:67441971-67442538	T-47D	breast:	n/a	n/a
41	MAX	chr11:67441849-67442530	MCF-7	breast:	n/a	chr11:67442124-67442133
42	EP300	chr11:67441996-67442591	ECC-1	luminal epithelium:	n/a	n/a
43	TEAD4	chr11:67441924-67442540	ECC-1	luminal epithelium:	n/a	n/a
44	CEBPB	chr11:67441909-67442438	ECC-1	luminal epithelium:	n/a	n/a
45	NFIC	chr11:67441895-67442592	ECC-1	luminal epithelium:	n/a	n/a
46	ELF1	chr11:67441797-67442661	MCF-7	breast:	n/a	n/a
47	POLR2A	chr11:67441906-67442284	MCF-7	breast:	n/a	n/a
48	CEBPB	chr11:67441830-67442484	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:67437911..67440480-chr11:67441652..67443889,5	MCF-7	breast:
2	chr11:67438405..67443993-chr11:67447780..67452157,7	MCF-7	breast:
3	chr11:67397074..67400069-chr11:67440700..67443508,3	K562	blood:
4	chr11:67434481..67439568-chr11:67439660..67443258,9	MCF-7	breast:
5	chr11:67433386..67435111-chr11:67439487..67442786,3	MCF-7	breast:
6	chr11:67397074..67400069-chr11:67440700..67443508,2	K562	blood:

Variant related genes	Relation type
ALDH3B2	TF binding region
ENSG00000239559	Chromatin interaction
ENSG00000132746	Chromatin interaction
ENSG00000167799	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10736660	0.86[MEX][hapmap]
rs11604041	0.85[EUR][1000 genomes]
rs1551886	1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes]
rs1551888	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes]
rs17510687	1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1903829	1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs1979375	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs1979376	0.82[AMR][1000 genomes]
rs2252577	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs2447598	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2509719	0.80[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2514053	0.85[EUR][1000 genomes]
rs3127	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes]
rs4646818	0.97[EUR][1000 genomes]
rs4646823	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes]
rs4930211	0.80[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes]
rs4930212	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4930465	0.82[AMR][1000 genomes]
rs61894527	0.84[EUR][1000 genomes]
rs61894528	0.84[EUR][1000 genomes]
rs7114210	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs866907	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak 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	146 gene(s)	inside rSNPs	diseases
3	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1050463	chr11:67343421-67717338	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1038189	chr11:67345320-67749246	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv1047236	chr11:67345320-67764068	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription 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 target site	83 gene(s)	inside rSNPs	diseases
8	nsv555268	chr11:67346743-67752972	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription 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	81 gene(s)	inside rSNPs	diseases
9	nsv1036101	chr11:67346813-67828351	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
10	nsv541079	chr11:67346813-67828351	Enhancers Flanking Active TSS Active TSS Weak transcription 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 miRNA target site	139 gene(s)	inside rSNPs	diseases
11	nsv1053811	chr11:67349444-67749246	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	esv1817852	chr11:67349899-67626567	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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 target site	69 gene(s)	inside rSNPs	diseases
13	nsv468606	chr11:67352689-67816936	Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
14	nsv555269	chr11:67352689-67816936	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
15	nsv897816	chr11:67353579-67460529	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1041887	chr11:67357365-67464893	Flanking Active TSS Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
17	nsv541080	chr11:67357365-67464893	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	nsv529452	chr11:67358204-67465721	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
19	nsv492253	chr11:67358204-67574402	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
20	nsv1043487	chr11:67360899-67662476	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
21	nsv897820	chr11:67372477-67460529	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
22	nsv897823	chr11:67378594-67460529	Enhancers Bivalent Enhancer Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
23	nsv897825	chr11:67381110-67460529	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
24	nsv897826	chr11:67408791-67462549	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv555274	chr11:67433869-67752972	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
26	esv1810710	chr11:67437879-67442661	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7947978	ZFPL1	cis	cerebellum	SCAN
rs7947978	CTSW	cis	cerebellum	SCAN
rs7947978	HRASLS2	cis	cerebellum	SCAN
rs7947978	BRMS1	cis	cerebellum	SCAN
rs7947978	LRP5	cis	cerebellum	SCAN
rs7947978	DPP3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67434000-67442400	Weak transcription	Fetal Intestine Small	intestine
2	chr11:67440800-67443200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:67441000-67442200	Active TSS	Esophagus	oesophagus
4	chr11:67441000-67442200	Flanking Active TSS	Placenta	Placenta
5	chr11:67441200-67442200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:67441200-67443200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr11:67441200-67443400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:67441400-67442200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:67441400-67442600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:67441400-67443000	Enhancers	NHEK	skin
11	chr11:67441400-67443400	Enhancers	Stomach Mucosa	stomach
12	chr11:67441600-67443200	Enhancers	Gastric	stomach
13	chr11:67441600-67443200	Enhancers	Pancreas	Pancrea
14	chr11:67441600-67443200	Enhancers	HMEC	breast
15	chr11:67441800-67442200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:67441800-67442800	Enhancers	Colonic Mucosa	Colon
17	chr11:67441800-67442800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr11:67442000-67442200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
19	chr11:67442000-67442200	Enhancers	Dnd41	blood
20	chr11:67442000-67442600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr11:67442000-67442600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:67442000-67443200	Enhancers	Rectal Mucosa Donor 31	rectum

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