Variant report

Variant	rs2957085
Chromosome Location	chr8:1692005-1692006
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:1690345..1695334-chr8:1710001..1714375,16	MCF-7	breast:
2	chr8:1682754..1684809-chr8:1691291..1693773,2	MCF-7	breast:
3	chr8:1690830..1693396-chr8:1731671..1734648,2	K562	blood:
4	chr8:1691117..1696538-chr8:1710667..1714961,13	MCF-7	breast:
5	chr8:1690439..1692118-chr8:1706880..1708703,2	MCF-7	breast:
6	chr8:1691840..1698609-chr8:1701330..1706354,17	MCF-7	breast:
7	chr8:1691178..1695166-chr8:1727484..1730315,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182372	Chromatin interaction
ENSG00000253982	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10087654	0.88[ASN][1000 genomes]
rs10095548	0.82[ASN][1000 genomes]
rs10095696	0.82[ASN][1000 genomes]
rs10097891	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10100341	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10102731	0.88[ASN][1000 genomes]
rs10105317	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10106153	0.93[ASN][1000 genomes]
rs10109098	0.83[ASN][1000 genomes]
rs10113471	0.95[ASN][1000 genomes]
rs10481354	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11136421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11136422	0.96[ASN][1000 genomes]
rs11136424	0.81[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11778824	0.87[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs11986414	0.86[GIH][hapmap]
rs12335115	0.95[ASN][1000 genomes]
rs12335117	0.82[ASN][1000 genomes]
rs12674711	0.92[ASN][1000 genomes]
rs13251071	0.96[ASN][1000 genomes]
rs13256424	0.83[ASN][1000 genomes]
rs13261755	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13282161	0.81[ASN][1000 genomes]
rs13540	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293977	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28376731	0.89[ASN][1000 genomes]
rs2977197	0.88[ASN][1000 genomes]
rs3812477	0.94[JPT][hapmap]
rs4242538	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4242539	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4370560	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4372027	0.87[ASN][1000 genomes]
rs4595147	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4639549	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4875806	0.81[ASN][1000 genomes]
rs4875889	0.95[ASN][1000 genomes]
rs4875957	0.81[ASN][1000 genomes]
rs4875958	0.81[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6558518	0.93[ASN][1000 genomes]
rs6558520	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6558521	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6558522	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6558523	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6558524	0.93[ASN][1000 genomes]
rs6558525	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6558526	0.91[ASN][1000 genomes]
rs6558527	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558528	0.92[ASN][1000 genomes]
rs6558531	0.87[ASN][1000 genomes]
rs6558532	0.87[ASN][1000 genomes]
rs6558533	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6558534	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6558535	0.87[ASN][1000 genomes]
rs6981804	0.93[ASN][1000 genomes]
rs6982516	0.83[ASN][1000 genomes]
rs6984632	0.91[ASN][1000 genomes]
rs6986102	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6991773	0.82[ASN][1000 genomes]
rs6991783	0.82[ASN][1000 genomes]
rs6993706	0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7000162	0.82[ASN][1000 genomes]
rs7001282	0.93[ASN][1000 genomes]
rs7005592	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7005699	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7008465	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7014327	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7014823	0.82[ASN][1000 genomes]
rs7015858	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs71499040	0.83[ASN][1000 genomes]
rs730377	0.87[ASN][1000 genomes]
rs730379	0.86[ASN][1000 genomes]
rs7341635	0.83[ASN][1000 genomes]
rs7459507	0.92[ASN][1000 genomes]
rs7460230	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7460287	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7460365	0.94[ASN][1000 genomes]
rs7460866	0.84[ASN][1000 genomes]
rs7460972	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7461159	0.81[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7461259	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7461600	0.81[ASN][1000 genomes]
rs7463876	0.88[ASN][1000 genomes]
rs7463879	0.86[ASN][1000 genomes]
rs7818406	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7822816	0.86[ASN][1000 genomes]
rs7827009	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs7827285	0.87[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs7828950	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7838456	0.87[ASN][1000 genomes]
rs7842425	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7844748	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7845723	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs7846610	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9022	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1031375	chr8:1320657-1722050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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 miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv889711	chr8:1591412-1904157	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv934075	chr8:1626857-1736355	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1034490	chr8:1654716-1782467	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv609527	chr8:1681733-1753497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
13	nsv870096	chr8:1682851-1767342	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
14	nsv465274	chr8:1685064-1728292	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv609528	chr8:1685064-1728292	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv532892	chr8:1687433-1839578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	esv2755149	chr8:1689290-1755281	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2957085	CTD-2336O2.1	cis	Thyroid	GTEx
rs2957085	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs2957085	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs2957085	CLN8	cis	parietal	SCAN
rs2957085	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs2957085	CTD-2336O2.1	cis	Esophagus Muscularis	GTEx
rs2957085	CLN8	cis	cerebellum	SCAN
rs2957085	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1685200-1692400	Weak transcription	Brain Substantia Nigra	brain
2	chr8:1686800-1692400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:1690600-1692400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:1691000-1692400	Weak transcription	Primary B cells from cord blood	blood
5	chr8:1691000-1693000	Weak transcription	K562	blood
6	chr8:1691200-1692800	Bivalent Enhancer	HepG2	liver
7	chr8:1691600-1693200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr8:1691600-1693400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr8:1691800-1692200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr8:1692000-1694000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr8:1692000-1694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:1692000-1694200	Enhancers	Esophagus	oesophagus
13	chr8:1692000-1694800	Enhancers	Spleen	Spleen

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