Variant report

Variant	rs1530625
Chromosome Location	chr2:46658067-46658068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46633942..46636424-chr2:46657432..46659768,2	K562	blood:
2	chr2:46655601..46658738-chr2:47401405..47405423,5	K562	blood:
3	chr2:46633942..46636867-chr2:46657432..46660033,3	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11125074	0.98[ASN][1000 genomes]
rs11125077	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12473626	0.85[CEU][hapmap]
rs12619420	0.82[EUR][1000 genomes]
rs12619985	0.82[ASN][1000 genomes]
rs12986585	0.83[ASN][1000 genomes]
rs12994892	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13009087	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13017856	0.85[EUR][1000 genomes]
rs13018019	0.85[EUR][1000 genomes]
rs13018477	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025174	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs13032473	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.87[EUR][1000 genomes]
rs13033917	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1447565	0.85[ASN][1000 genomes]
rs1530627	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530628	0.90[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1542271	0.92[CEU][hapmap];0.81[CHD][hapmap];0.82[EUR][1000 genomes]
rs1597041	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868080	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1868096	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2053765	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2084345	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2121697	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2121700	0.81[CEU][hapmap]
rs2166745	0.83[ASN][1000 genomes]
rs2197698	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276555	0.85[CEU][hapmap]
rs2346177	0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs2346178	0.82[ASN][1000 genomes]
rs2881327	0.81[ASN][1000 genomes]
rs34186951	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814047	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs3814048	0.88[EUR][1000 genomes]
rs3863000	0.82[EUR][1000 genomes]
rs4366955	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4396767	0.84[CEU][hapmap]
rs4413204	0.83[ASN][1000 genomes]
rs4456747	0.85[EUR][1000 genomes]
rs4953373	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4953374	0.85[ASN][1000 genomes]
rs4953377	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953381	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953384	0.88[EUR][1000 genomes]
rs4953385	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs4953389	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs62138876	0.81[ASN][1000 genomes]
rs6544894	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715279	0.82[EUR][1000 genomes]
rs6726089	0.87[GIH][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs6728611	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6728847	0.87[EUR][1000 genomes]
rs6737959	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556828	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]
rs7559484	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562332	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7565770	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7565850	0.82[EUR][1000 genomes]
rs7571742	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7587138	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7588586	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7588938	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598507	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7598584	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7598712	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv457330	chr2:46637081-46660752	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv581744	chr2:46637081-46660752	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	nsv961402	chr2:46656702-46658194	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1530625	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs1530625	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs1530625	CRIPT	cis	lymphoblastoid	seeQTL
rs1530625	ATP6V1E2	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46647800-46658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:46656600-46661600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:46656600-46661800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:46657200-46672200	Enhancers	HepG2	liver
5	chr2:46657600-46658400	Weak transcription	Placenta	Placenta
6	chr2:46657600-46660600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:46657600-46660800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:46657600-46663800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:46657800-46658200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46657800-46660600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:46658000-46658200	Flanking Active TSS	K562	blood
12	chr2:46658000-46659800	Enhancers	Dnd41	blood
13	chr2:46658000-46660600	Enhancers	Primary T cells from cord blood	blood
14	chr2:46658000-46660800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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