Variant report

Variant	rs1530627
Chromosome Location	chr2:46670146-46670147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46661044..46663217-chr2:46670020..46671893,2	MCF-7	breast:
2	chr2:46633572..46635870-chr2:46669679..46671465,2	MCF-7	breast:
3	chr2:46541786..46543916-chr2:46667813..46670793,2	K562	blood:
4	chr2:46668595..46671087-chr2:46674345..46676657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241791	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11125074	0.91[ASN][1000 genomes]
rs11125077	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12473626	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs12619420	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12986585	0.82[ASN][1000 genomes]
rs12994892	0.84[ASN][1000 genomes]
rs13009087	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13017856	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13018019	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13018477	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13025174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025967	0.81[EUR][1000 genomes]
rs13032473	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13033917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1447565	0.83[ASN][1000 genomes]
rs1530625	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	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542271	1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1597041	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868080	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868096	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084345	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2121697	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2121700	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2166745	0.82[ASN][1000 genomes]
rs2197698	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276555	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap]
rs2346177	0.91[GIH][hapmap];0.80[ASN][1000 genomes]
rs2346178	0.80[ASN][1000 genomes]
rs34186951	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3814047	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3814048	0.90[EUR][1000 genomes]
rs3863000	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4366955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4396767	0.83[CEU][hapmap]
rs4413204	0.81[ASN][1000 genomes]
rs4456747	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4953373	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4953374	0.83[ASN][1000 genomes]
rs4953377	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953381	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4953384	0.90[EUR][1000 genomes]
rs4953385	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4953389	0.92[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs6544894	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6715279	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6726089	0.91[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs6728611	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728847	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6737959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556828	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]
rs7557998	0.94[ASW][hapmap];0.84[CEU][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs7559484	0.84[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562332	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7565770	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7565850	0.83[EUR][1000 genomes]
rs7571742	0.84[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587138	0.91[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7588586	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7588938	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7598507	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598584	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598712	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1530627	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs1530627	CRIPT	cis	lymphoblastoid	seeQTL
rs1530627	CRIPT	cis	parietal	SCAN
rs1530627	ATP6V1E2	cis	multi-tissue	Pritchard
rs1530627	CRIPT	cis	multi-tissue	Pritchard
rs1530627	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs1530627	ATP6V1E2	cis	parietal	SCAN

Chromatin state (count:12 , 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	chr2:46663200-46671400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:46668000-46670600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:46668200-46683600	Weak transcription	K562	blood
7	chr2:46669600-46670200	Enhancers	Pancreas	Pancrea
8	chr2:46669600-46671400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:46669800-46670200	Enhancers	Esophagus	oesophagus
10	chr2:46670000-46670200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr2:46670000-46670200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:46670000-46675400	Weak transcription	Gastric	stomach

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