Variant report

Variant	rs760675
Chromosome Location	chr6:5693007-5693008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1001568	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1005521	0.81[CHD][hapmap]
rs11752777	0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12190311	0.81[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs12210617	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12216327	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13213128	0.84[CHB][hapmap]
rs2142738	0.85[CEU][hapmap];0.89[CHB][hapmap];0.80[EUR][1000 genomes]
rs2326634	0.82[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs4140654	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959347	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs4960125	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6918561	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs6918675	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935719	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739358	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742697	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746913	0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs877010	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs878988	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9328328	0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9378439	0.89[ASN][1000 genomes]
rs9378979	0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs9378980	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs9378983	0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[ASN][1000 genomes]
rs9405281	0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs9405859	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap]
rs9405861	0.84[CHB][hapmap]
rs9502329	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9504488	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.98[MKK][hapmap]

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	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3473790	chr6:5692573-5707035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3473791	chr6:5692573-5707035	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv823407	chr6:5692735-5706712	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs760675	NQO2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
5	chr6:5678200-5694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:5678400-5693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:5680600-5695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:5680800-5695000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:5681800-5695000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:5682200-5693200	Weak transcription	Primary T cells from cord blood	blood
11	chr6:5682400-5695200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:5682400-5695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:5684600-5695400	Weak transcription	Fetal Stomach	stomach
14	chr6:5684800-5696000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:5684800-5706000	Weak transcription	Ovary	ovary
16	chr6:5685000-5695400	Weak transcription	HSMMtube	muscle
17	chr6:5685000-5698600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:5691400-5698200	Weak transcription	Spleen	Spleen
19	chr6:5692000-5693200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:5692600-5695000	Weak transcription	Dnd41	blood
21	chr6:5692800-5701400	Weak transcription	Right Atrium	heart
22	chr6:5693000-5696000	Weak transcription	Fetal Intestine Small	intestine

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