Variant report

Variant	rs295579
Chromosome Location	chr5:60419751-60419752
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60417821..60420681-chr5:60456901..60458465,2	MCF-7	breast:
2	chr5:60412981..60415103-chr5:60419112..60420959,2	K562	blood:

Variant related genes	Relation type
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10471502	0.87[AFR][1000 genomes]
rs10514906	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10939882	0.87[EUR][1000 genomes]
rs11951076	0.88[EUR][1000 genomes]
rs11957772	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs124898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12518865	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13168191	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13171576	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1382914	0.85[EUR][1000 genomes]
rs158564	0.88[EUR][1000 genomes]
rs158570	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs158571	0.83[EUR][1000 genomes]
rs158572	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs158699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs158914	1.00[JPT][hapmap]
rs158915	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs158919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs158921	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs158923	0.85[EUR][1000 genomes]
rs158924	0.85[EUR][1000 genomes]
rs158931	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs158932	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs158933	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs158934	0.83[EUR][1000 genomes]
rs158935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs158936	0.83[EUR][1000 genomes]
rs158937	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs159357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs159358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159371	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs159374	0.91[AFR][1000 genomes]
rs159375	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs159376	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159377	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159378	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159380	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159537	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs162234	0.88[EUR][1000 genomes]
rs162238	0.87[EUR][1000 genomes]
rs162241	0.86[EUR][1000 genomes]
rs162242	0.87[EUR][1000 genomes]
rs162244	0.86[EUR][1000 genomes]
rs162247	0.85[EUR][1000 genomes]
rs162248	0.85[EUR][1000 genomes]
rs172348	0.85[EUR][1000 genomes]
rs172945	0.87[EUR][1000 genomes]
rs182410	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs185354	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs187459	0.94[EUR][1000 genomes]
rs2080869	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2112365	0.87[EUR][1000 genomes]
rs2263514	0.85[EUR][1000 genomes]
rs2270822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs248677	0.91[EUR][1000 genomes]
rs248682	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs248683	0.84[AFR][1000 genomes]
rs248685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545475	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545478	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545503	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256375	0.90[AFR][1000 genomes]
rs256376	0.83[AFR][1000 genomes]
rs2650512	0.85[EUR][1000 genomes]
rs2650517	0.85[EUR][1000 genomes]
rs2694518	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2694530	0.85[EUR][1000 genomes]
rs2694531	0.85[EUR][1000 genomes]
rs290503	0.87[EUR][1000 genomes]
rs290506	0.87[EUR][1000 genomes]
rs290507	0.87[EUR][1000 genomes]
rs290516	0.82[EUR][1000 genomes]
rs2950235	0.85[EUR][1000 genomes]
rs295522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs295524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs295531	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295532	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295533	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295551	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295559	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295560	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs295561	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295563	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295564	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295566	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295569	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs295573	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295578	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs295582	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs298629	0.86[EUR][1000 genomes]
rs3108388	0.86[EUR][1000 genomes]
rs329622	0.87[EUR][1000 genomes]
rs329623	0.87[EUR][1000 genomes]
rs329625	0.87[EUR][1000 genomes]
rs329626	0.84[EUR][1000 genomes]
rs34593	0.91[EUR][1000 genomes]
rs34609	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs34610	0.85[AFR][1000 genomes]
rs34613	0.86[EUR][1000 genomes]
rs34614	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34616	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs34617	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs34621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs34624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34625	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs34636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34637	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34639	0.94[EUR][1000 genomes]
rs34643	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs34644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs39661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40084	0.94[EUR][1000 genomes]
rs40421	0.84[AFR][1000 genomes]
rs4141502	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4647045	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4699969	0.87[EUR][1000 genomes]
rs4700406	0.83[AFR][1000 genomes]
rs56159106	0.82[EUR][1000 genomes]
rs56409036	0.86[EUR][1000 genomes]
rs6868884	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6869073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6878124	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6886481	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs723276	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7701839	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7706753	0.88[EUR][1000 genomes]
rs7718028	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7721096	0.83[EUR][1000 genomes]
rs7723754	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs810883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs810884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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 target site	42 gene(s)	inside rSNPs	diseases
2	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs295579	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60395400-60428200	Weak transcription	HSMMtube	muscle
2	chr5:60396800-60420400	Weak transcription	Ovary	ovary
3	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:60402800-60420600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:60411200-60420600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:60411200-60422400	Weak transcription	Aorta	Aorta
7	chr5:60415600-60421800	Weak transcription	Esophagus	oesophagus
8	chr5:60417200-60449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:60419400-60420000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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