Variant report

Variant	rs34617
Chromosome Location	chr5:60476705-60476706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60456770..60459746-chr5:60476085..60478262,2	K562	blood:
2	chr5:60475085..60478138-chr5:60478979..60482831,4	K562	blood:
3	chr5:60464303..60466155-chr5:60475802..60477971,2	K562	blood:
4	chr5:60471591..60474041-chr5:60476246..60478290,2	MCF-7	breast:
5	chr5:60464643..60466155-chr5:60475802..60478493,2	K562	blood:
6	chr5:60473979..60476884-chr5:60480404..60482643,2	MCF-7	breast:
7	chr5:60454738..60463245-chr5:60465333..60477980,25	K562	blood:
8	chr5:60472733..60477448-chr5:60625158..60628299,7	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10939882	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951076	0.96[AFR][1000 genomes];0.91[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]
rs12518792	0.82[AFR][1000 genomes]
rs12518865	0.87[EUR][1000 genomes]
rs13168191	0.87[EUR][1000 genomes]
rs13171576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382914	0.81[EUR][1000 genomes]
rs1460961	0.87[YRI][hapmap]
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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[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	0.81[AFR][1000 genomes];0.85[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	0.85[AFR][1000 genomes];0.96[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613	0.87[AFR][1000 genomes];0.99[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];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619	0.83[YRI][hapmap]
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];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[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	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159106	0.91[AFR][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	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713481	0.81[AFR][1000 genomes]
rs7721096	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7737276	0.83[AFR][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
rs34617	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	chr5:60474200-60476800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:60476400-60477200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:60476400-60477200	Active TSS	NHLF	lung
5	chr5:60476400-60477400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:60476600-60477000	Active TSS	Primary hematopoietic stem cells	blood
7	chr5:60476600-60477000	Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:60476600-60477200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:60476600-60477200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:60476600-60477200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr5:60476600-60477200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:60476600-60477200	Active TSS	Fetal Lung	lung
13	chr5:60476600-60477200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr5:60476600-60477200	Active TSS	Right Atrium	heart
15	chr5:60476600-60477200	Flanking Active TSS	Dnd41	blood
16	chr5:60476600-60477200	Active TSS	GM12878-XiMat	blood
17	chr5:60476600-60477200	Active TSS	HUVEC	blood vessel
18	chr5:60476600-60477400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:60476600-60477400	Active TSS	A549	lung
20	chr5:60476600-60477600	Active TSS	Duodenum Smooth Muscle	Duodenum

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