Variant report

Variant	rs9405859
Chromosome Location	chr6:5676459-5676460
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	chr6:5670035..5672305-chr6:5675850..5677415,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1001568	0.89[CHB][hapmap]
rs11752777	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13213128	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2142738	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2326634	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140654	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs4959347	0.85[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4960125	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4960126	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62385480	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62408067	0.86[ASN][1000 genomes]
rs6918383	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918561	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs6918675	0.85[CHB][hapmap]
rs760675	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap]
rs7739358	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs7746913	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs877010	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878988	0.85[CHB][hapmap]
rs9328328	0.88[CHB][hapmap]
rs9378979	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378980	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378983	0.85[CHB][hapmap]
rs9392709	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9392710	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9405281	0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs9405861	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9504488	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]

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
rs9405859	NQO2	cis	parietal	SCAN
rs9405859	C6orf201	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5653200-5677600	Weak transcription	Gastric	stomach
2	chr6:5654600-5677600	Weak transcription	Pancreas	Pancrea
3	chr6:5665200-5677800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:5671800-5680000	Weak transcription	HepG2	liver
5	chr6:5672000-5677400	Weak transcription	Fetal Heart	heart
6	chr6:5672200-5679600	Weak transcription	Primary B cells from cord blood	blood
7	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
8	chr6:5672400-5676800	Weak transcription	Stomach Mucosa	stomach
9	chr6:5672400-5679200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:5672400-5685600	Weak transcription	Aorta	Aorta
11	chr6:5672600-5678800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:5672600-5679800	Weak transcription	GM12878-XiMat	blood
13	chr6:5672600-5680000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:5673200-5679400	Weak transcription	Fetal Kidney	kidney
15	chr6:5673200-5679800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:5673200-5680200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:5673400-5679600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:5673400-5679800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:5673600-5679200	Weak transcription	Spleen	Spleen
20	chr6:5673800-5676600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:5673800-5676800	Weak transcription	HMEC	breast
22	chr6:5673800-5676800	Weak transcription	NHEK	skin
23	chr6:5673800-5677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:5673800-5679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:5673800-5682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:5674000-5676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:5674000-5676800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:5674000-5677600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:5674000-5678000	Weak transcription	Primary T cells from cord blood	blood
32	chr6:5674000-5678000	Weak transcription	Right Atrium	heart
33	chr6:5674000-5678800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:5674000-5679600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:5674000-5680400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:5674000-5680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:5674000-5681800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:5674200-5679400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:5674400-5683600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:5674800-5676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:5674800-5676800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:5674800-5677400	Weak transcription	NHLF	lung
43	chr6:5674800-5677800	Weak transcription	Adipose Nuclei	Adipose
44	chr6:5674800-5679200	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:5674800-5680200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:5674800-5680400	Weak transcription	Left Ventricle	heart
47	chr6:5674800-5681600	Weak transcription	Fetal Thymus	thymus
48	chr6:5675200-5676800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:5675200-5677000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:5675200-5677000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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