Variant report

Variant	rs13003074
Chromosome Location	chr2:46671420-46671421
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46661044..46663217-chr2:46670020..46671893,2	MCF-7	breast:
2	chr2:46633572..46635870-chr2:46669679..46671465,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11125075	0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs12986653	0.86[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12986899	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991646	0.89[ASN][1000 genomes]
rs13002880	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13007688	0.86[CEU][hapmap];0.81[MEX][hapmap]
rs13010062	0.91[ASN][1000 genomes]
rs13010097	1.00[JPT][hapmap]
rs13020043	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13024414	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13030579	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs1447563	0.89[JPT][hapmap];0.81[MEX][hapmap]
rs1530621	0.95[CEU][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1530624	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530628	0.87[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1597040	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1900591	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2084679	1.00[JPT][hapmap]
rs2121698	0.91[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2121700	0.91[ASW][hapmap];0.84[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2346414	1.00[JPT][hapmap]
rs2346415	1.00[JPT][hapmap]
rs34712412	0.89[ASN][1000 genomes]
rs34791442	0.91[ASN][1000 genomes]
rs34854267	0.91[EUR][1000 genomes]
rs35462976	0.85[ASN][1000 genomes]
rs35509718	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36006825	0.91[EUR][1000 genomes]
rs4312543	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4396767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4549147	0.89[EUR][1000 genomes]
rs4563285	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953365	0.89[ASN][1000 genomes]
rs4953371	0.87[ASN][1000 genomes]
rs4953372	0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs4953377	0.82[EUR][1000 genomes]
rs4953379	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953387	0.86[CEU][hapmap];0.85[MEX][hapmap]
rs4953388	0.86[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4953390	0.86[CEU][hapmap];0.85[MEX][hapmap]
rs56048837	0.96[ASN][1000 genomes]
rs6544895	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6718875	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6749877	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6757564	0.90[EUR][1000 genomes]
rs718849	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7556828	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs7565188	0.88[EUR][1000 genomes]
rs7565770	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs880671	0.81[CEU][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13003074	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs13003074	ATP6V1E2	cis	multi-tissue	Pritchard
rs13003074	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs13003074	CRIPT	cis	parietal	SCAN
rs13003074	CRIPT	cis	lymphoblastoid	seeQTL
rs13003074	CRIPT	cis	multi-tissue	Pritchard
rs13003074	RHOQ	cis	cerebellum	SCAN
rs13003074	ATP6V1E2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46657200-46672200	Enhancers	HepG2	liver
2	chr2:46662200-46678400	Weak transcription	Placenta	Placenta
3	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:46668200-46683600	Weak transcription	K562	blood
5	chr2:46670000-46675400	Weak transcription	Gastric	stomach
6	chr2:46671000-46672200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:46671400-46671600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:46671400-46672200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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