Variant report

Variant	rs2953517
Chromosome Location	chr8:87332013-87332014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87232045..87233654-chr8:87330272..87332535,2	MCF-7	breast:
2	chr8:87327910..87330150-chr8:87330958..87333182,2	MCF-7	breast:
3	chr8:87329069..87335338-chr8:87352769..87359177,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254231	Chromatin interaction
ENSG00000123124	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10086340	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10093238	0.82[JPT][hapmap]
rs10093729	0.84[ASN][1000 genomes]
rs10095129	0.82[JPT][hapmap]
rs10095498	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10096443	0.82[JPT][hapmap]
rs10097450	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10103691	0.80[JPT][hapmap]
rs11775728	0.82[JPT][hapmap]
rs12546802	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs12549332	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12550142	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs12679811	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs12681287	0.95[CEU][hapmap]
rs13042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13249753	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13254675	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13262672	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13263353	0.87[CEU][hapmap]
rs13267782	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13269259	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs13280468	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13281414	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2953509	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2953510	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2953511	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2953516	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976177	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976178	0.86[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976179	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2976181	0.97[ASN][1000 genomes]
rs2976201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4129535	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4464946	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4490816	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4587306	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4623392	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4961188	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4961193	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4961194	0.82[JPT][hapmap]
rs4961195	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs4961196	0.81[JPT][hapmap]
rs6415565	0.82[JPT][hapmap]
rs6471296	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6471309	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6471354	0.81[JPT][hapmap]
rs6471360	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6985066	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6996052	0.82[JPT][hapmap]
rs7003059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006017	0.82[JPT][hapmap]
rs7006629	0.82[JPT][hapmap]
rs7015490	0.82[JPT][hapmap]
rs7017706	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs7017716	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7017719	0.82[JPT][hapmap]
rs71503461	0.80[ASN][1000 genomes]
rs7460286	0.82[JPT][hapmap]
rs7460439	0.82[JPT][hapmap]
rs7461413	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7465046	0.83[ASN][1000 genomes]
rs7465511	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7816275	0.85[ASN][1000 genomes]
rs7820234	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7820697	0.81[JPT][hapmap]
rs7832493	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7833786	0.95[CEU][hapmap]
rs7837569	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7839601	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs7841690	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7846090	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs9942792	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9942823	0.91[CHB][hapmap];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	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1023114	chr8:87167184-87335197	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1033960	chr8:87167790-87334194	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1016050	chr8:87167790-87335197	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1023772	chr8:87177368-87334194	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1031874	chr8:87177368-87335197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1030401	chr8:87177368-87337260	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv2761445	chr8:87185470-87335197	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv519507	chr8:87187195-87333968	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	esv3360246	chr8:87200232-87419244	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv611708	chr8:87205885-87333968	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1017535	chr8:87261702-87367934	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2953517	FAM82B	cis	Brain Pons	GTEx
rs2953517	RMDN1	cis	Whole Blood	GTEx
rs2953517	FAM82B	cis	lesional skin	skin_eQTL
rs2953517	WWP1	cis	multi-tissue	Pritchard
rs2953517	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87318400-87333200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:87328400-87332200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:87328400-87332400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:87328600-87332400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:87328600-87333800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr8:87328600-87333800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr8:87329600-87332200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr8:87330800-87334800	Enhancers	Fetal Lung	lung
9	chr8:87331000-87332200	Enhancers	Liver	Liver
10	chr8:87331200-87332200	Weak transcription	Placenta	Placenta
11	chr8:87331200-87332200	Weak transcription	Ovary	ovary
12	chr8:87331200-87334400	Weak transcription	Esophagus	oesophagus
13	chr8:87331400-87333400	Weak transcription	Psoas Muscle	Psoas
14	chr8:87331800-87332200	Enhancers	Adipose Nuclei	Adipose
15	chr8:87331800-87332200	Enhancers	A549	lung
16	chr8:87332000-87332200	Enhancers	Brain Anterior Caudate	brain
17	chr8:87332000-87332200	Enhancers	Colon Smooth Muscle	Colon
18	chr8:87332000-87332200	Enhancers	HepG2	liver

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