Variant report

Variant	rs2080869
Chromosome Location	chr5:60388578-60388579
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 206 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:199)

rs_ID	r²[population]
rs10064187	0.91[ASN][1000 genomes]
rs10076937	0.86[ASN][1000 genomes]
rs1038144	0.80[ASN][1000 genomes]
rs10471502	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514906	0.88[ASN][1000 genomes]
rs10939882	0.88[EUR][1000 genomes]
rs11744756	0.80[ASN][1000 genomes]
rs11951076	0.87[EUR][1000 genomes]
rs11957772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs124898	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12518865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522154	0.86[ASN][1000 genomes]
rs13155076	0.86[ASN][1000 genomes]
rs13168191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171576	0.88[EUR][1000 genomes]
rs1382914	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158564	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158570	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158571	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158696	0.94[ASN][1000 genomes]
rs158697	0.94[ASN][1000 genomes]
rs158699	0.94[ASN][1000 genomes]
rs158700	0.94[ASN][1000 genomes]
rs158914	0.97[ASN][1000 genomes]
rs158915	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158918	0.91[ASN][1000 genomes]
rs158919	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158922	0.97[ASN][1000 genomes]
rs158923	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158924	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158927	0.91[ASN][1000 genomes]
rs158929	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158931	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158932	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158933	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158934	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158935	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158936	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158937	0.91[ASN][1000 genomes]
rs158938	0.97[ASN][1000 genomes]
rs159357	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159358	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159371	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159374	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159375	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159376	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159377	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159378	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159380	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159537	0.87[EUR][1000 genomes]
rs162228	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162234	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162238	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162241	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162242	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162243	0.91[ASN][1000 genomes]
rs162244	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162246	0.91[ASN][1000 genomes]
rs162247	0.89[EUR][1000 genomes]
rs162248	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162251	1.00[ASN][1000 genomes]
rs168710	1.00[ASN][1000 genomes]
rs16878547	0.94[ASN][1000 genomes]
rs16878548	0.94[ASN][1000 genomes]
rs169700	1.00[ASN][1000 genomes]
rs172348	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820082	0.81[ASN][1000 genomes]
rs182410	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs185354	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs187459	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989653	0.94[ASN][1000 genomes]
rs2112365	0.88[EUR][1000 genomes]
rs2120954	0.86[ASN][1000 genomes]
rs2120955	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2263514	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270822	0.88[ASN][1000 genomes]
rs248677	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248682	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248683	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248685	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248688	1.00[ASN][1000 genomes]
rs2545475	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545478	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545493	0.85[ASN][1000 genomes]
rs2545503	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256375	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256376	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590570	0.86[ASN][1000 genomes]
rs2619890	1.00[ASN][1000 genomes]
rs2619893	1.00[ASN][1000 genomes]
rs2650506	0.81[EUR][1000 genomes]
rs2650512	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650517	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694518	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2694528	0.94[ASN][1000 genomes]
rs2694530	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407266	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290503	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290506	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290507	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290511	0.94[ASN][1000 genomes]
rs290513	1.00[ASN][1000 genomes]
rs290514	0.91[ASN][1000 genomes]
rs290515	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290516	0.86[EUR][1000 genomes]
rs2950235	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295522	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295524	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295531	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295532	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs295533	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295551	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295559	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs295560	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295561	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295563	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295564	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295566	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295569	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295573	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295578	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295579	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295582	0.87[EUR][1000 genomes]
rs298629	0.87[EUR][1000 genomes]
rs3101879	1.00[ASN][1000 genomes]
rs3108388	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117	0.86[ASN][1000 genomes]
rs329622	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329623	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329624	1.00[ASN][1000 genomes]
rs329625	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329626	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34591	1.00[ASN][1000 genomes]
rs34592	1.00[ASN][1000 genomes]
rs34593	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34609	0.87[EUR][1000 genomes]
rs34610	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34613	0.87[EUR][1000 genomes]
rs34614	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34616	0.87[EUR][1000 genomes]
rs34617	0.87[EUR][1000 genomes]
rs34621	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34623	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34624	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34625	0.88[EUR][1000 genomes]
rs34636	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34637	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34638	1.00[ASN][1000 genomes]
rs34639	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34643	1.00[ASN][1000 genomes]
rs34644	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35546392	0.83[ASN][1000 genomes]
rs35617853	0.80[ASN][1000 genomes]
rs35766700	0.86[ASN][1000 genomes]
rs35948426	0.86[ASN][1000 genomes]
rs39661	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40084	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40421	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235483	0.86[ASN][1000 genomes]
rs4235484	0.86[ASN][1000 genomes]
rs42437	1.00[ASN][1000 genomes]
rs4546327	0.80[ASN][1000 genomes]
rs4647102	0.86[ASN][1000 genomes]
rs4647138	0.86[ASN][1000 genomes]
rs4647139	0.86[ASN][1000 genomes]
rs4647151	0.80[ASN][1000 genomes]
rs4647162	0.81[ASN][1000 genomes]
rs4699967	0.88[ASN][1000 genomes]
rs4699969	0.88[EUR][1000 genomes]
rs4700406	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409036	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59292447	0.88[ASN][1000 genomes]
rs59797139	0.83[ASN][1000 genomes]
rs6862622	0.88[ASN][1000 genomes]
rs6863749	0.88[ASN][1000 genomes]
rs6868884	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869073	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869454	0.88[ASN][1000 genomes]
rs6878124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885989	0.86[ASN][1000 genomes]
rs6886481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893210	0.88[ASN][1000 genomes]
rs723276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7706753	0.86[EUR][1000 genomes]
rs7712364	0.88[ASN][1000 genomes]
rs7718028	0.88[ASN][1000 genomes]
rs7721096	0.80[EUR][1000 genomes]
rs7723754	0.88[ASN][1000 genomes]
rs810883	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs810884	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9291702	0.94[ASN][1000 genomes]
rs929780	0.80[ASN][1000 genomes]
rs976080	0.86[ASN][1000 genomes]
rs9763418	0.86[ASN][1000 genomes]
rs976581	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	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
5	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2080869	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
2	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:60366400-60397400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:60367400-60399400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:60367600-60398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:60367800-60403800	Weak transcription	Primary B cells from cord blood	blood
7	chr5:60368200-60390600	Weak transcription	Fetal Intestine Small	intestine
8	chr5:60368200-60397600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:60368200-60402000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:60368400-60390200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:60369000-60400200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:60369800-60396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:60370200-60395600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:60371600-60398000	Weak transcription	HSMM	muscle
15	chr5:60373200-60395600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:60378800-60395600	Weak transcription	Primary T cells from cord blood	blood
17	chr5:60378800-60403400	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:60379400-60395600	Weak transcription	Ovary	ovary
19	chr5:60379400-60403000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:60381000-60419400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:60381400-60397600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:60383000-60395600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:60387200-60395600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:60387600-60391200	Weak transcription	Spleen	Spleen
25	chr5:60387800-60395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:60387800-60396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:60388000-60394000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:60388200-60399200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:60388400-60401400	Weak transcription	Fetal Intestine Large	intestine

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