Variant report

Variant	rs3802519
Chromosome Location	chr10:28341714-28341715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10763642	0.88[CEU][hapmap]
rs10826389	0.86[ASN][1000 genomes]
rs10826397	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs10826398	0.88[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11006818	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11006821	0.89[CEU][hapmap]
rs11006822	0.89[CEU][hapmap]
rs11006825	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11006830	0.89[CEU][hapmap]
rs11006832	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs11006833	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006834	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006836	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006839	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006840	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006841	0.81[ASN][1000 genomes]
rs11006843	0.86[CEU][hapmap]
rs11006852	0.89[CEU][hapmap]
rs11006869	0.88[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs11006877	0.88[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs11006883	0.82[CEU][hapmap]
rs12217744	0.89[ASN][1000 genomes]
rs12253376	0.89[CEU][hapmap]
rs1317790	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs1574418	0.89[CEU][hapmap]
rs17757844	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs2887213	0.81[ASN][1000 genomes]
rs3802520	0.89[CEU][hapmap]
rs3802521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802523	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3885634	0.89[CEU][hapmap]
rs3885635	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs59082756	0.80[ASN][1000 genomes]
rs6481499	0.89[CEU][hapmap]
rs7071369	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7895285	0.88[CEU][hapmap]
rs7898270	0.88[CEU][hapmap]
rs7898482	0.88[CEU][hapmap]
rs7903192	0.88[CEU][hapmap]
rs7919895	0.80[CEU][hapmap]
rs927676	1.00[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1052182	chr10:28259142-28361830	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv894988	chr10:28337570-28410989	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3802519	GSTM3	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28330000-28345000	Weak transcription	Pancreas	Pancrea
2	chr10:28331200-28345000	Weak transcription	Aorta	Aorta
3	chr10:28334800-28341800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:28335000-28345800	Weak transcription	Brain Angular Gyrus	brain
5	chr10:28335600-28345000	Weak transcription	Fetal Stomach	stomach
6	chr10:28336200-28349400	Weak transcription	Gastric	stomach
7	chr10:28336400-28346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:28336600-28345600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:28336800-28346600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:28337400-28341800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:28337400-28342600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:28337400-28347400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:28337600-28342400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr10:28337800-28345000	Weak transcription	Fetal Intestine Small	intestine
15	chr10:28337800-28346000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:28338200-28345000	Weak transcription	Left Ventricle	heart
17	chr10:28338400-28345000	Weak transcription	Esophagus	oesophagus
18	chr10:28338600-28342600	Weak transcription	NHDF-Ad	bronchial
19	chr10:28338800-28341800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:28338800-28342400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:28339000-28345000	Weak transcription	Lung	lung
22	chr10:28339800-28342400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:28339800-28345000	Weak transcription	Primary T cells from cord blood	blood
24	chr10:28340200-28342400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:28340800-28342400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:28341200-28350000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:28341200-28377600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:28341400-28346400	Weak transcription	Spleen	Spleen
29	chr10:28341600-28342600	Weak transcription	Rectal Smooth Muscle	rectum

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