Variant report

Variant	rs34613
Chromosome Location	chr5:60478558-60478559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60470829..60473385-chr5:60478345..60480116,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFAF2-2	chr5:60476586-60479163	NONHSAT101661

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10939882	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951076	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957772	0.87[EUR][1000 genomes]
rs124898	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs12518865	0.87[EUR][1000 genomes]
rs12653132	0.82[AFR][1000 genomes]
rs13168191	0.87[EUR][1000 genomes]
rs13171576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382914	0.81[EUR][1000 genomes]
rs158564	0.82[EUR][1000 genomes]
rs158923	0.81[EUR][1000 genomes]
rs158924	0.81[EUR][1000 genomes]
rs159358	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs159376	0.84[EUR][1000 genomes]
rs159377	0.86[EUR][1000 genomes]
rs159378	0.86[EUR][1000 genomes]
rs159380	0.86[EUR][1000 genomes]
rs159537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162234	0.82[EUR][1000 genomes]
rs162238	0.81[EUR][1000 genomes]
rs162241	0.81[EUR][1000 genomes]
rs162242	0.82[EUR][1000 genomes]
rs162244	0.81[EUR][1000 genomes]
rs162247	0.80[EUR][1000 genomes]
rs172348	0.81[EUR][1000 genomes]
rs172945	0.81[EUR][1000 genomes]
rs182410	0.86[EUR][1000 genomes]
rs185354	0.81[EUR][1000 genomes]
rs187459	0.85[EUR][1000 genomes]
rs2080869	0.87[EUR][1000 genomes]
rs2112365	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263514	0.81[EUR][1000 genomes]
rs248677	0.82[EUR][1000 genomes]
rs248682	0.87[EUR][1000 genomes]
rs248685	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2545475	0.87[EUR][1000 genomes]
rs2545478	0.87[EUR][1000 genomes]
rs2545503	0.85[EUR][1000 genomes]
rs2650512	0.81[EUR][1000 genomes]
rs2650517	0.81[EUR][1000 genomes]
rs2694530	0.81[EUR][1000 genomes]
rs2694531	0.81[EUR][1000 genomes]
rs290503	0.81[EUR][1000 genomes]
rs290506	0.81[EUR][1000 genomes]
rs290507	0.81[EUR][1000 genomes]
rs2950235	0.81[EUR][1000 genomes]
rs295522	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs295532	0.84[EUR][1000 genomes]
rs295533	0.87[EUR][1000 genomes]
rs295551	0.87[EUR][1000 genomes]
rs295560	0.86[EUR][1000 genomes]
rs295566	0.87[EUR][1000 genomes]
rs295569	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs295579	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs298629	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108388	0.81[EUR][1000 genomes]
rs329622	0.81[EUR][1000 genomes]
rs329623	0.81[EUR][1000 genomes]
rs329625	0.81[EUR][1000 genomes]
rs329626	0.80[EUR][1000 genomes]
rs34593	0.82[EUR][1000 genomes]
rs34609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614	0.88[EUR][1000 genomes]
rs34616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs34624	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs34625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34636	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs34637	0.86[EUR][1000 genomes]
rs34639	0.85[EUR][1000 genomes]
rs34644	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs39661	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs40084	0.85[EUR][1000 genomes]
rs4141502	0.87[EUR][1000 genomes]
rs4699969	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159106	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56409036	0.81[EUR][1000 genomes]
rs6878124	0.87[EUR][1000 genomes]
rs6886481	0.87[EUR][1000 genomes]
rs723276	0.87[EUR][1000 genomes]
rs7701839	0.86[EUR][1000 genomes]
rs7706753	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721096	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs810883	0.85[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs34613	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60468600-60484400	Weak transcription	Aorta	Aorta
2	chr5:60477200-60479000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:60477200-60479000	Enhancers	Dnd41	blood
4	chr5:60477200-60480200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:60477200-60480400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:60477200-60480400	Weak transcription	HUVEC	blood vessel
7	chr5:60477200-60480400	Weak transcription	NHDF-Ad	bronchial
8	chr5:60477200-60480400	Weak transcription	NHLF	lung
9	chr5:60477200-60483800	Weak transcription	Right Atrium	heart
10	chr5:60477400-60480400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:60477600-60478600	Enhancers	A549	lung
12	chr5:60477600-60480000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:60478000-60478600	Enhancers	Primary T cells from cord blood	blood
14	chr5:60478200-60478600	Enhancers	Adipose Nuclei	Adipose
15	chr5:60478200-60478600	Enhancers	K562	blood
16	chr5:60478200-60478800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:60478400-60478800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:60478400-60478800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:60478400-60478800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr5:60478400-60479000	Enhancers	Fetal Lung	lung

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