Variant report

Variant	rs9504488
Chromosome Location	chr6:5682429-5682430
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5666510..5668168-chr6:5681628..5683242,2	K562	blood:
2	chr6:5678900..5683178-chr6:5683336..5687695,5	K562	blood:
3	chr6:5679376..5681001-chr6:5681268..5682896,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1001568	0.89[CHB][hapmap]
rs11752777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213128	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2005970	0.82[ASN][1000 genomes]
rs2142738	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2326634	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140654	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs4959347	0.85[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4960125	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4960126	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62385480	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62408067	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6918383	0.81[ASN][1000 genomes]
rs6918561	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap]
rs6918675	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs760675	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.98[MKK][hapmap]
rs7739358	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap]
rs7746913	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs877010	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878988	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap]
rs9328328	0.88[CHB][hapmap]
rs9378979	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378980	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9378983	0.85[CHB][hapmap]
rs9392709	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9392710	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9405280	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9405281	0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs9405859	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9405861	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9504488	NQO2	cis	parietal	SCAN
rs9504488	C6orf201	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5672400-5685600	Weak transcription	Aorta	Aorta
3	chr6:5673800-5682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:5674400-5683600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:5678000-5686200	Weak transcription	Gastric	stomach
8	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
9	chr6:5678200-5694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:5678400-5693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:5678600-5686600	Weak transcription	Right Atrium	heart
12	chr6:5680600-5682600	Enhancers	Primary B cells from cord blood	blood
13	chr6:5680600-5684600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:5680600-5684600	Weak transcription	Spleen	Spleen
15	chr6:5680600-5695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:5680800-5684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:5680800-5684400	Weak transcription	HSMMtube	muscle
18	chr6:5680800-5687600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:5680800-5695000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:5681800-5695000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:5682200-5693200	Weak transcription	Primary T cells from cord blood	blood
22	chr6:5682400-5684400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:5682400-5684400	Weak transcription	NHDF-Ad	bronchial
24	chr6:5682400-5684400	Weak transcription	Osteobl	bone
25	chr6:5682400-5695200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:5682400-5695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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