Variant report

Variant	rs17816345
Chromosome Location	chr15:33067339-33067340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11629595	1.00[JPT][hapmap]
rs11631339	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11632119	1.00[JPT][hapmap]
rs11632555	1.00[JPT][hapmap]
rs11853746	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12148200	1.00[ASN][1000 genomes]
rs12442768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12901405	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12906330	1.00[JPT][hapmap]
rs12911544	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs12915737	0.81[TSI][hapmap]
rs17816333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816387	1.00[JPT][hapmap]
rs2123068	1.00[JPT][hapmap]
rs28595770	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002618	0.82[ASN][1000 genomes]
rs9806641	0.83[CHD][hapmap];1.00[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	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 target site	10 gene(s)	inside rSNPs	diseases
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv832961	chr15:33021177-33134988	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv903977	chr15:33040782-33117302	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2763090	chr15:33042338-33072151	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17816345	ARHGAP11A	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33058200-33069800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:33060600-33097600	Weak transcription	Thymus	Thymus
3	chr15:33061200-33070200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:33061200-33141000	Weak transcription	Placenta	Placenta
5	chr15:33062400-33068600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:33062400-33068800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:33062600-33069600	Weak transcription	Stomach Mucosa	stomach
8	chr15:33062600-33111200	Weak transcription	Gastric	stomach
9	chr15:33063000-33069200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:33063200-33082400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:33063600-33068600	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:33063800-33094400	Weak transcription	Fetal Stomach	stomach
13	chr15:33064000-33067400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:33064000-33067400	Enhancers	NHDF-Ad	bronchial
15	chr15:33064000-33068400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:33064000-33069800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:33064000-33070600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:33064800-33074000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:33065000-33067400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:33065000-33068000	Genic enhancers	Osteobl	bone
21	chr15:33065400-33067400	Enhancers	NH-A	brain
22	chr15:33065400-33070600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:33065600-33067600	Genic enhancers	HSMM	muscle
24	chr15:33065800-33067400	Weak transcription	Esophagus	oesophagus
25	chr15:33065800-33067600	Weak transcription	Lung	lung
26	chr15:33065800-33098600	Weak transcription	Colonic Mucosa	Colon
27	chr15:33066000-33068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:33066000-33068800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:33066200-33067400	Enhancers	HSMMtube	muscle
30	chr15:33066200-33069200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:33066600-33067400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr15:33066600-33068200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:33066800-33067400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:33066800-33067400	Enhancers	A549	lung
35	chr15:33066800-33070800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:33067000-33068400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:33067000-33070600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:33067200-33071000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:33067200-33077800	Weak transcription	NHLF	lung
40	chr15:33067200-33089000	Weak transcription	Rectal Mucosa Donor 29	rectum

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