Variant report

Variant	rs811496
Chromosome Location	chr10:28619487-28619488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11006935	0.82[CHB][hapmap]
rs11006941	0.82[CHB][hapmap]
rs11006942	0.82[CHB][hapmap]
rs1148177	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148178	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148179	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148180	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148181	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1148185	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148187	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1148189	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12098315	0.96[ASN][1000 genomes]
rs12098714	0.81[ASN][1000 genomes]
rs12098807	0.96[ASN][1000 genomes]
rs12254745	0.82[CHB][hapmap]
rs1249340	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1249347	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1249348	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1273097	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1379320	0.86[ASN][1000 genomes]
rs16928633	0.82[CHB][hapmap]
rs1762188	0.86[ASN][1000 genomes]
rs2100614	1.00[CHB][hapmap]
rs2447629	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2995539	0.86[ASN][1000 genomes]
rs34827546	0.96[ASN][1000 genomes]
rs61845947	0.86[ASN][1000 genomes]
rs703017	0.88[AFR][1000 genomes]
rs7078271	0.82[CHB][hapmap]
rs7100335	0.82[CHB][hapmap]
rs72803699	0.93[ASN][1000 genomes]
rs72805609	0.93[ASN][1000 genomes]
rs72805627	0.96[ASN][1000 genomes]
rs72805630	0.96[ASN][1000 genomes]
rs72805631	0.93[ASN][1000 genomes]
rs7898888	1.00[JPT][hapmap]
rs7911615	0.82[CHB][hapmap]
rs7916525	0.82[CHB][hapmap]
rs813081	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1044938	chr10:28601993-28659440	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs811496	ARHGAP12	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28614800-28620600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:28615000-28620000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr10:28615200-28621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:28616000-28619600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:28616000-28621600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:28616200-28619800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr10:28616400-28620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:28616800-28620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:28616800-28623000	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:28616800-28623800	Weak transcription	NHLF	lung
11	chr10:28617000-28620600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:28617000-28621000	Enhancers	Colon Smooth Muscle	Colon
13	chr10:28617000-28621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:28617000-28621600	Weak transcription	Pancreas	Pancrea
15	chr10:28617000-28622800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:28617200-28621000	Weak transcription	NH-A	brain
17	chr10:28617400-28621000	Weak transcription	HMEC	breast
18	chr10:28617600-28621000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:28617600-28621000	Weak transcription	HSMM	muscle
20	chr10:28617800-28621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:28617800-28622600	Weak transcription	NHEK	skin
22	chr10:28617800-28623000	Weak transcription	Fetal Stomach	stomach
23	chr10:28618000-28620200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr10:28618200-28619800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:28618200-28620600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr10:28618200-28621000	Weak transcription	HSMMtube	muscle
27	chr10:28618200-28621200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr10:28618600-28620800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr10:28618600-28621600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:28618600-28621800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr10:28618800-28619600	Enhancers	Primary T cells from cord blood	blood
32	chr10:28618800-28620600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr10:28618800-28621000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr10:28618800-28621000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr10:28618800-28621000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:28618800-28621800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr10:28618800-28624400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr10:28618800-28626600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:28619000-28620000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr10:28619000-28621200	Enhancers	Primary B cells from cord blood	blood
41	chr10:28619000-28621800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:28619000-28624600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr10:28619200-28619800	Enhancers	Fetal Thymus	thymus
44	chr10:28619200-28624600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr10:28619400-28621200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:28619400-28624600	Enhancers	Primary hematopoietic stem cells	blood

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