Variant report

Variant	rs159380
Chromosome Location	chr5:60428781-60428782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 192 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10064187	0.97[ASN][1000 genomes]
rs10076937	0.91[ASN][1000 genomes]
rs1038144	0.86[ASN][1000 genomes]
rs10471502	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514906	0.94[ASN][1000 genomes]
rs10939882	0.87[EUR][1000 genomes]
rs11744756	0.86[ASN][1000 genomes]
rs11951076	0.88[EUR][1000 genomes]
rs11957772	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs124898	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518865	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168191	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13171576	0.87[EUR][1000 genomes]
rs13359074	0.82[ASN][1000 genomes]
rs1382914	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158564	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158570	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158571	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158696	0.88[ASN][1000 genomes]
rs158697	0.88[ASN][1000 genomes]
rs158699	0.88[ASN][1000 genomes]
rs158700	0.88[ASN][1000 genomes]
rs158914	0.91[ASN][1000 genomes]
rs158915	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158918	0.86[ASN][1000 genomes]
rs158919	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158922	0.91[ASN][1000 genomes]
rs158923	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158924	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158927	0.97[ASN][1000 genomes]
rs158929	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158931	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158932	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs158933	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158934	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158935	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158936	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158937	0.86[ASN][1000 genomes]
rs158938	0.91[ASN][1000 genomes]
rs159357	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159358	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159371	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159374	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159375	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159376	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159537	0.86[EUR][1000 genomes]
rs162228	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162234	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162238	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162241	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162242	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162243	0.86[ASN][1000 genomes]
rs162244	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162246	0.86[ASN][1000 genomes]
rs162247	0.88[EUR][1000 genomes]
rs162248	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162251	0.94[ASN][1000 genomes]
rs168710	0.94[ASN][1000 genomes]
rs16878547	0.88[ASN][1000 genomes]
rs16878548	0.88[ASN][1000 genomes]
rs169700	0.94[ASN][1000 genomes]
rs172348	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs172945	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1820082	0.86[ASN][1000 genomes]
rs182410	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185354	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs187459	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1989653	0.88[ASN][1000 genomes]
rs2080869	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2112365	0.87[EUR][1000 genomes]
rs2120954	0.91[ASN][1000 genomes]
rs2120955	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2263514	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270822	0.94[ASN][1000 genomes]
rs248677	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248682	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248683	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248685	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248688	0.94[ASN][1000 genomes]
rs2545475	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545478	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545493	0.85[ASN][1000 genomes]
rs2545503	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256375	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256376	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590570	0.91[ASN][1000 genomes]
rs2619890	0.94[ASN][1000 genomes]
rs2619893	0.94[ASN][1000 genomes]
rs2650506	0.80[EUR][1000 genomes]
rs2650512	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2650517	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694518	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2694528	0.88[ASN][1000 genomes]
rs2694530	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694531	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28407266	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290503	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290506	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290507	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290511	0.88[ASN][1000 genomes]
rs290513	0.94[ASN][1000 genomes]
rs290514	0.97[ASN][1000 genomes]
rs290515	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290516	0.85[EUR][1000 genomes]
rs2950235	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295522	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295524	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295531	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295532	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295533	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295551	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295559	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs295560	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295561	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295563	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295564	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295566	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295569	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295573	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295578	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295579	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs295582	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs298629	0.86[EUR][1000 genomes]
rs3101879	0.94[ASN][1000 genomes]
rs3108388	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329622	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329623	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329624	0.94[ASN][1000 genomes]
rs329625	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329626	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34591	0.94[ASN][1000 genomes]
rs34592	0.94[ASN][1000 genomes]
rs34593	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34609	0.86[EUR][1000 genomes]
rs34610	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613	0.86[EUR][1000 genomes]
rs34614	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34616	0.86[EUR][1000 genomes]
rs34617	0.86[EUR][1000 genomes]
rs34621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34623	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34625	0.87[EUR][1000 genomes]
rs34636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638	0.94[ASN][1000 genomes]
rs34639	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34643	0.94[ASN][1000 genomes]
rs34644	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35948426	0.91[ASN][1000 genomes]
rs39661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40084	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40421	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4141502	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235483	0.91[ASN][1000 genomes]
rs4235484	0.91[ASN][1000 genomes]
rs42437	0.94[ASN][1000 genomes]
rs4647102	0.91[ASN][1000 genomes]
rs4699967	0.83[ASN][1000 genomes]
rs4699969	0.87[EUR][1000 genomes]
rs4700406	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700410	0.85[ASN][1000 genomes]
rs56159106	0.80[EUR][1000 genomes]
rs56409036	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59292447	0.94[ASN][1000 genomes]
rs6862622	0.94[ASN][1000 genomes]
rs6863749	0.94[ASN][1000 genomes]
rs6868884	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869073	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869454	0.94[ASN][1000 genomes]
rs6878124	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6886481	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893210	0.94[ASN][1000 genomes]
rs723276	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701839	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7706753	0.87[EUR][1000 genomes]
rs7712364	0.94[ASN][1000 genomes]
rs7718028	0.94[ASN][1000 genomes]
rs7721096	0.81[EUR][1000 genomes]
rs7723754	0.94[ASN][1000 genomes]
rs810883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs810884	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291702	0.88[ASN][1000 genomes]
rs929780	0.86[ASN][1000 genomes]
rs976080	0.91[ASN][1000 genomes]
rs976581	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs159380	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60417200-60449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:60426800-60431600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:60428000-60428800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:60428000-60428800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:60428000-60429000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:60428000-60429000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:60428000-60429000	Enhancers	HSMM	muscle
9	chr5:60428000-60429200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:60428200-60428800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:60428200-60429000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:60428200-60429000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:60428200-60429000	Enhancers	HSMMtube	muscle
14	chr5:60428200-60429800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:60428400-60428800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:60428400-60429000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:60428600-60452000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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