Variant report

Variant	rs2121700
Chromosome Location	chr2:46675665-46675666
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	GATA3	chr2:46675490-46676219	MCF-7	breast:	n/a	n/a
2	MAFK	chr2:46675527-46675676	HepG2	liver:	n/a	n/a
3	GATA3	chr2:46675648-46676231	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RN7SL817P	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11125075	0.93[GIH][hapmap]
rs12986899	0.89[EUR][1000 genomes]
rs13002880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003074	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13007688	1.00[JPT][hapmap]
rs13011721	1.00[JPT][hapmap]
rs13018477	0.84[CEU][hapmap]
rs13020043	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13024414	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025174	0.88[CEU][hapmap]
rs13032473	0.88[CEU][hapmap]
rs13033917	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs1530621	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530624	0.84[EUR][1000 genomes]
rs1530625	0.81[CEU][hapmap]
rs1530627	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1542271	0.88[CEU][hapmap]
rs1597040	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900591	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053765	0.80[EUR][1000 genomes]
rs2084345	0.80[EUR][1000 genomes]
rs2121697	0.82[CEU][hapmap]
rs2121698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34854267	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35509718	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36006825	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3814047	0.88[CEU][hapmap]
rs4312543	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366955	0.80[EUR][1000 genomes]
rs4396767	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4549147	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563285	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4952830	1.00[JPT][hapmap]
rs4953372	0.90[GIH][hapmap]
rs4953379	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4953381	0.80[EUR][1000 genomes]
rs4953385	0.88[CEU][hapmap]
rs4953387	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4953390	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6544895	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544898	1.00[JPT][hapmap]
rs6718875	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737959	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs6749877	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6757564	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718849	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559484	0.80[CEU][hapmap]
rs7562332	0.84[CEU][hapmap]
rs7565188	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7571742	0.80[CEU][hapmap]
rs7588938	0.83[CEU][hapmap]
rs7598584	0.80[CEU][hapmap]
rs880671	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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
12	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2121700	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs2121700	CRIPT	cis	lymphoblastoid	seeQTL
rs2121700	ATP6V1E2	cis	multi-tissue	Pritchard
rs2121700	CRIPT	cis	parietal	SCAN
rs2121700	CRIPT	cis	multi-tissue	Pritchard
rs2121700	ATP6V1E2	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46662200-46678400	Weak transcription	Placenta	Placenta
2	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:46668200-46683600	Weak transcription	K562	blood
4	chr2:46674600-46678400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:46674600-46686600	Weak transcription	NHLF	lung
6	chr2:46675400-46676400	Enhancers	Adipose Nuclei	Adipose
7	chr2:46675400-46676800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:46675400-46677200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:46675400-46677200	Enhancers	Hela-S3	cervix
10	chr2:46675600-46678800	Weak transcription	Gastric	stomach

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