Variant report

Variant	rs11990117
Chromosome Location	chr8:61605768-61605769
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61604857..61607132-chr8:61609872..61611507,2	MCF-7	breast:
2	chr8:61599708..61602124-chr8:61603749..61606422,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10808711	0.86[ASN][1000 genomes]
rs10808712	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10808713	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10957154	0.95[ASN][1000 genomes]
rs10957155	0.95[ASN][1000 genomes]
rs10957156	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11985638	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11992809	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11993480	0.84[ASN][1000 genomes]
rs11995234	0.86[ASN][1000 genomes]
rs11997122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12544305	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs12681737	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13255519	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1384688	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16926407	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035456	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035457	0.95[ASN][1000 genomes]
rs2128713	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4307377	0.89[CHB][hapmap]
rs4449834	0.89[CHB][hapmap]
rs4472560	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4526395	1.00[CHB][hapmap]
rs4737563	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4737565	0.89[CHB][hapmap]
rs4738815	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4738818	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4738831	0.89[CHB][hapmap]
rs4738832	0.89[CHB][hapmap]
rs6471894	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6471896	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs6471897	0.84[ASN][1000 genomes]
rs6471898	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6471903	0.89[CHB][hapmap]
rs6471905	0.89[CHB][hapmap]
rs6988582	0.85[CEU][hapmap]
rs6995557	0.95[ASN][1000 genomes]
rs7000766	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7005873	0.89[CHB][hapmap]
rs7011972	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs730085	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7814114	0.84[ASN][1000 genomes]
rs7816126	0.84[ASN][1000 genomes]
rs7816621	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7826035	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7834977	0.86[CHB][hapmap]
rs7836586	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7840098	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7842389	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7842498	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7845701	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs900502	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9643371	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv824657	chr8:61555227-61626758	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv824658	chr8:61561488-61612108	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1027929	chr8:61569620-61617812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1017564	chr8:61577791-61617812	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv526196	chr8:61593569-61877623	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv1019809	chr8:61597918-61624034	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv539631	chr8:61597918-61624034	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv6219	chr8:61599770-61644558	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11990117	TOX	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61593400-61607200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:61594000-61610400	Weak transcription	A549	lung
3	chr8:61594200-61617600	Weak transcription	Hela-S3	cervix
4	chr8:61597000-61619800	Weak transcription	HMEC	breast
5	chr8:61597400-61607400	Weak transcription	Small Intestine	intestine
6	chr8:61597800-61606600	Weak transcription	Adipose Nuclei	Adipose
7	chr8:61598000-61606000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:61598000-61609000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:61598000-61609600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:61598200-61619800	Weak transcription	HepG2	liver
11	chr8:61598800-61608000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr8:61599200-61613200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:61599400-61605800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr8:61600200-61612200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:61601800-61607400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr8:61602200-61605800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr8:61602600-61606400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr8:61602600-61606800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr8:61602600-61606800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr8:61602600-61606800	Weak transcription	Fetal Lung	lung
21	chr8:61602600-61607000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:61602600-61607400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:61602600-61610800	Weak transcription	Fetal Intestine Small	intestine
24	chr8:61603400-61605800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr8:61603400-61606000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr8:61603400-61606400	Weak transcription	Fetal Heart	heart
27	chr8:61603400-61610200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr8:61603400-61613400	Weak transcription	K562	blood
29	chr8:61603400-61616200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr8:61603400-61620600	Weak transcription	Fetal Intestine Large	intestine
31	chr8:61603400-61626200	Weak transcription	Fetal Thymus	thymus
32	chr8:61603800-61607600	Enhancers	Primary T cells from cord blood	blood
33	chr8:61603800-61608200	Enhancers	Brain Germinal Matrix	brain
34	chr8:61604000-61605800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr8:61604000-61607400	Enhancers	Brain Hippocampus Middle	brain
36	chr8:61604200-61606400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr8:61604400-61606400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr8:61604400-61606600	Enhancers	Primary B cells from cord blood	blood
39	chr8:61604400-61614200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr8:61604600-61607400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr8:61604600-61609000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr8:61604800-61605800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:61605200-61605800	Enhancers	Fetal Brain Female	brain
44	chr8:61605200-61606000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr8:61605200-61606200	Enhancers	Lung	lung
46	chr8:61605200-61606200	Enhancers	Pancreas	Pancrea
47	chr8:61605200-61607400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:61605200-61607400	Enhancers	Brain Cingulate Gyrus	brain
49	chr8:61605200-61607400	Enhancers	Gastric	stomach
50	chr8:61605200-61607600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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