Variant report

Variant	rs12505291
Chromosome Location	chr4:87511571-87511572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87510138..87512928-chr4:87514603..87517692,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163629	Chromatin interaction
ENSG00000109339	Chromatin interaction

Extended variants
information (count: 188 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:179)

rs_ID	r²[population]
rs10000891	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10001010	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10001986	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10002511	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10003989	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10009119	1.00[ASN][1000 genomes]
rs10009309	1.00[ASN][1000 genomes]
rs10009603	1.00[ASN][1000 genomes]
rs10009758	1.00[ASN][1000 genomes]
rs10009789	1.00[ASN][1000 genomes]
rs10013048	1.00[ASN][1000 genomes]
rs10013114	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10013988	1.00[ASN][1000 genomes]
rs10016082	1.00[ASN][1000 genomes]
rs10016120	1.00[ASN][1000 genomes]
rs10016124	1.00[ASN][1000 genomes]
rs10020590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10021168	1.00[ASN][1000 genomes]
rs10023163	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10024496	1.00[ASN][1000 genomes]
rs10024631	1.00[ASN][1000 genomes]
rs10024860	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10025930	1.00[ASN][1000 genomes]
rs10026645	1.00[ASN][1000 genomes]
rs10028003	1.00[ASN][1000 genomes]
rs10028357	1.00[ASN][1000 genomes]
rs10028550	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10029055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10029565	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10030981	1.00[ASN][1000 genomes]
rs10032126	1.00[ASN][1000 genomes]
rs10032979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10033029	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10033679	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10084899	1.00[ASN][1000 genomes]
rs10084902	1.00[ASN][1000 genomes]
rs10084954	1.00[ASN][1000 genomes]
rs10212681	1.00[ASN][1000 genomes]
rs10212723	1.00[ASN][1000 genomes]
rs10213021	1.00[ASN][1000 genomes]
rs10213484	1.00[ASN][1000 genomes]
rs10213632	1.00[ASN][1000 genomes]
rs1038290	1.00[ASN][1000 genomes]
rs10470883	1.00[ASN][1000 genomes]
rs10470933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10516780	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10516783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10516784	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097119	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12171330	1.00[ASN][1000 genomes]
rs12171331	1.00[ASN][1000 genomes]
rs12171388	1.00[ASN][1000 genomes]
rs12171414	1.00[ASN][1000 genomes]
rs12171415	1.00[ASN][1000 genomes]
rs12171445	1.00[ASN][1000 genomes]
rs12171459	1.00[ASN][1000 genomes]
rs12171474	1.00[ASN][1000 genomes]
rs12498653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498681	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12499206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12499471	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12499477	1.00[ASN][1000 genomes]
rs12499575	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12499984	1.00[ASN][1000 genomes]
rs12499991	1.00[ASN][1000 genomes]
rs12500797	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12502376	1.00[ASN][1000 genomes]
rs12502487	1.00[AMR][1000 genomes]
rs12502645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507034	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12507163	1.00[ASN][1000 genomes]
rs12508156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12508339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12508545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12508579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12508626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12509039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509430	1.00[AMR][1000 genomes]
rs12509560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12510393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511153	1.00[ASN][1000 genomes]
rs12511318	1.00[ASN][1000 genomes]
rs12512524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12512858	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12710827	1.00[ASN][1000 genomes]
rs13108514	1.00[ASN][1000 genomes]
rs13108571	1.00[ASN][1000 genomes]
rs13108581	1.00[ASN][1000 genomes]
rs13108735	1.00[ASN][1000 genomes]
rs13109164	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13111757	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13112139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13112150	1.00[ASN][1000 genomes]
rs13115122	1.00[ASN][1000 genomes]
rs13115681	1.00[ASN][1000 genomes]
rs13117481	1.00[ASN][1000 genomes]
rs13118632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13120724	1.00[ASN][1000 genomes]
rs13131069	1.00[ASN][1000 genomes]
rs13135528	1.00[ASN][1000 genomes]
rs13136201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13136651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13148078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13148807	1.00[ASN][1000 genomes]
rs13150561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13152382	1.00[ASN][1000 genomes]
rs1420620	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17454432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17454655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28411302	1.00[ASN][1000 genomes]
rs28416315	1.00[ASN][1000 genomes]
rs28421178	1.00[ASN][1000 genomes]
rs28441099	1.00[ASN][1000 genomes]
rs28448567	1.00[ASN][1000 genomes]
rs28483600	1.00[ASN][1000 genomes]
rs28491390	1.00[ASN][1000 genomes]
rs28502328	1.00[ASN][1000 genomes]
rs28535818	1.00[ASN][1000 genomes]
rs28545322	1.00[ASN][1000 genomes]
rs28548225	1.00[ASN][1000 genomes]
rs28570548	1.00[ASN][1000 genomes]
rs28572183	1.00[ASN][1000 genomes]
rs28572787	1.00[ASN][1000 genomes]
rs28578632	1.00[ASN][1000 genomes]
rs28587332	1.00[ASN][1000 genomes]
rs28610135	1.00[ASN][1000 genomes]
rs28619493	1.00[ASN][1000 genomes]
rs28623441	1.00[ASN][1000 genomes]
rs28634740	1.00[ASN][1000 genomes]
rs28663463	1.00[ASN][1000 genomes]
rs28682899	1.00[ASN][1000 genomes]
rs28696860	1.00[ASN][1000 genomes]
rs28710769	1.00[ASN][1000 genomes]
rs28785508	1.00[ASN][1000 genomes]
rs28785868	1.00[ASN][1000 genomes]
rs28833029	1.00[ASN][1000 genomes]
rs28846151	1.00[ASN][1000 genomes]
rs28846800	1.00[ASN][1000 genomes]
rs28868582	1.00[ASN][1000 genomes]
rs28877076	1.00[ASN][1000 genomes]
rs34178790	1.00[ASN][1000 genomes]
rs34320168	1.00[ASN][1000 genomes]
rs34371873	1.00[ASN][1000 genomes]
rs35254293	1.00[ASN][1000 genomes]
rs35355289	1.00[ASN][1000 genomes]
rs35528563	1.00[ASN][1000 genomes]
rs35982123	1.00[ASN][1000 genomes]
rs66584788	1.00[ASN][1000 genomes]
rs67067959	1.00[ASN][1000 genomes]
rs6817630	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71605609	1.00[ASN][1000 genomes]
rs71605610	1.00[ASN][1000 genomes]
rs71605611	1.00[ASN][1000 genomes]
rs71605613	1.00[ASN][1000 genomes]
rs71605614	1.00[ASN][1000 genomes]
rs71605615	1.00[ASN][1000 genomes]
rs71605617	1.00[ASN][1000 genomes]
rs71605618	1.00[ASN][1000 genomes]
rs71633353	1.00[ASN][1000 genomes]
rs7664147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7664860	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7668637	1.00[ASN][1000 genomes]
rs7698481	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7699564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9307022	1.00[ASN][1000 genomes]
rs9307023	1.00[ASN][1000 genomes]
rs9307024	1.00[ASN][1000 genomes]
rs9884784	1.00[ASN][1000 genomes]
rs9990536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9993492	1.00[ASN][1000 genomes]
rs9993838	1.00[ASN][1000 genomes]
rs9994213	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9994421	1.00[ASN][1000 genomes]
rs9997453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87496600-87512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:87501600-87512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:87502400-87514200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:87503800-87513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:87503800-87513800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:87504000-87513400	Weak transcription	Brain Substantia Nigra	brain
7	chr4:87507600-87513200	Weak transcription	A549	lung
8	chr4:87507600-87514200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:87508000-87513400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:87508800-87513400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:87508800-87513400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:87508800-87513600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:87508800-87513800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:87508800-87514000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:87508800-87514400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:87508800-87514600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:87509000-87512600	Weak transcription	Fetal Kidney	kidney
18	chr4:87509000-87513200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:87509000-87513400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:87509000-87513400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:87509000-87513400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:87509000-87513600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:87509000-87513600	Weak transcription	Adipose Nuclei	Adipose
24	chr4:87509000-87513800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:87509200-87512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:87509200-87513400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:87509200-87513400	Weak transcription	HMEC	breast
28	chr4:87509200-87513600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:87509200-87514000	Weak transcription	Fetal Lung	lung
30	chr4:87510200-87512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:87510400-87513200	Weak transcription	NHEK	skin

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