Variant report

Variant	rs7556828
Chromosome Location	chr2:46663172-46663173
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	MAZ	chr2:46662894-46663265	K562	blood:	n/a	n/a
2	RCOR1	chr2:46662891-46663173	K562	blood:	n/a	n/a
3	POLR2A	chr2:46663014-46663400	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46661070..46664987-chr2:46768132..46770822,3	K562	blood:
2	chr2:46661044..46663217-chr2:46670020..46671893,2	MCF-7	breast:
3	chr2:46606421..46608528-chr2:46662722..46665704,2	K562	blood:

Variant related genes	Relation type
TMEM247	TF binding region
ENSG00000116016	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11125074	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11125077	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12619985	0.90[YRI][hapmap]
rs12986653	0.80[CEU][hapmap]
rs12986899	0.82[EUR][1000 genomes]
rs12994892	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13002880	0.86[CEU][hapmap]
rs13007688	0.80[CEU][hapmap]
rs13009087	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13017856	0.83[EUR][1000 genomes]
rs13018019	0.83[EUR][1000 genomes]
rs13018477	0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs13025174	0.80[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025967	0.87[EUR][1000 genomes]
rs13030579	0.80[CEU][hapmap]
rs13032473	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13033917	0.80[CEU][hapmap];0.95[CHB][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1530621	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs1530625	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530627	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530628	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1542271	0.80[CEU][hapmap]
rs1597041	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1868080	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1868096	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053765	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2084345	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2121697	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2121698	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2197698	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2346177	0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2346414	0.80[CEU][hapmap]
rs34186951	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814047	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs3814048	0.85[EUR][1000 genomes]
rs3863000	0.80[EUR][1000 genomes]
rs4366955	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4456747	0.83[EUR][1000 genomes]
rs4953373	0.83[ASN][1000 genomes]
rs4953377	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953381	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953384	0.86[EUR][1000 genomes]
rs4953385	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs4953387	0.80[CEU][hapmap]
rs4953388	0.80[CEU][hapmap]
rs4953389	0.83[CHB][hapmap]
rs4953390	0.80[CEU][hapmap]
rs6544894	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6726089	0.87[GIH][hapmap]
rs6728611	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6728847	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6737959	0.80[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7559484	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7562332	0.95[CHB][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs7565770	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571742	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587138	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs7588586	0.83[EUR][1000 genomes]
rs7588938	0.95[CHB][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs7598507	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7598584	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7598712	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active 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	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1001902	chr2:46651624-46675665	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997637	chr2:46651624-46676628	Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1003646	chr2:46651624-46677186	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
11	nsv581745	chr2:46660445-46693963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7556828	ATP6V1E2	cis	multi-tissue	Pritchard
rs7556828	CRIPT	cis	multi-tissue	Pritchard
rs7556828	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs7556828	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs7556828	CRIPT	cis	parietal	SCAN
rs7556828	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs7556828	ATP6V1E2	cis	parietal	SCAN
rs7556828	CRIPT	cis	lymphoblastoid	seeQTL
rs7556828	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46657200-46672200	Enhancers	HepG2	liver
2	chr2:46657600-46663800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:46659200-46665600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:46660400-46665600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:46660400-46665800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:46660400-46666200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:46660600-46665800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:46660600-46665800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:46660600-46665800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:46660800-46663800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46660800-46665200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:46660800-46665400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:46660800-46669600	Weak transcription	Pancreas	Pancrea
14	chr2:46661000-46663200	Enhancers	K562	blood
15	chr2:46661200-46663200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:46661200-46663400	Weak transcription	Small Intestine	intestine
17	chr2:46661200-46663800	Enhancers	HSMMtube	muscle
18	chr2:46661600-46663200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:46661600-46663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:46661600-46663400	Enhancers	HSMM	muscle
21	chr2:46661600-46663600	Enhancers	HMEC	breast
22	chr2:46661600-46664000	Enhancers	NHLF	lung
23	chr2:46661800-46663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:46661800-46663200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:46661800-46663200	Enhancers	NHEK	skin
26	chr2:46661800-46663600	Enhancers	Osteobl	bone
27	chr2:46661800-46663800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:46662000-46663200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:46662000-46663200	Enhancers	NH-A	brain
30	chr2:46662000-46663600	Enhancers	Fetal Lung	lung
31	chr2:46662200-46663200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:46662200-46663600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:46662200-46663800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:46662200-46666400	Weak transcription	Fetal Thymus	thymus
35	chr2:46662200-46678400	Weak transcription	Placenta	Placenta
36	chr2:46662400-46663200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:46662600-46665600	Weak transcription	Primary T cells from cord blood	blood
38	chr2:46662800-46665400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:46663000-46663200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:46663000-46663200	Enhancers	Fetal Muscle Leg	muscle
41	chr2:46663000-46663400	Enhancers	Fetal Heart	heart

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