Variant report

Variant	rs11196796
Chromosome Location	chr10:116352988-116352989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10159807	0.82[EUR][1000 genomes]
rs10159811	0.83[EUR][1000 genomes]
rs10159857	0.83[EUR][1000 genomes]
rs10749167	0.84[EUR][1000 genomes]
rs10749168	0.84[EUR][1000 genomes]
rs10787533	0.91[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10787534	0.82[EUR][1000 genomes]
rs10787535	0.84[EUR][1000 genomes]
rs10787538	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10885574	0.83[EUR][1000 genomes]
rs10885576	0.84[EUR][1000 genomes]
rs10885578	0.85[EUR][1000 genomes]
rs10885579	0.91[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10885581	0.88[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10885582	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10885583	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885585	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885586	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11196775	0.84[MEX][hapmap]
rs11196782	0.85[EUR][1000 genomes]
rs11196783	0.85[EUR][1000 genomes]
rs11196784	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11196786	0.90[EUR][1000 genomes]
rs11196790	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11196793	0.89[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11196794	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11196797	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12357781	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12772307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1333686	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1333690	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752016	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7893570	0.83[EUR][1000 genomes]
rs7923449	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11196796	VWA2	cis	parietal	SCAN
rs11196796	RAB11FIP2	cis	parietal	SCAN
rs11196796	ABLIM1	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116336800-116359800	Weak transcription	Lung	lung
2	chr10:116336800-116360000	Weak transcription	Fetal Muscle Leg	muscle
3	chr10:116337000-116360200	Weak transcription	Esophagus	oesophagus
4	chr10:116337600-116353000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:116337800-116362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:116341400-116356800	Weak transcription	Brain Anterior Caudate	brain
7	chr10:116342200-116359800	Weak transcription	Adipose Nuclei	Adipose
8	chr10:116345000-116382400	Weak transcription	HSMM	muscle
9	chr10:116345800-116364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr10:116346000-116356000	Weak transcription	Right Atrium	heart
11	chr10:116346200-116360000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:116346400-116355200	Weak transcription	Fetal Heart	heart
13	chr10:116347600-116357400	Weak transcription	Pancreas	Pancrea
14	chr10:116348600-116355800	Weak transcription	Right Ventricle	heart
15	chr10:116350600-116358800	Weak transcription	Liver	Liver
16	chr10:116351000-116353200	Weak transcription	Stomach Mucosa	stomach
17	chr10:116351600-116353600	Enhancers	Fetal Intestine Small	intestine
18	chr10:116352000-116353400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr10:116352000-116354000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr10:116352000-116354200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:116352200-116353400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr10:116352200-116353600	Enhancers	HepG2	liver
23	chr10:116352200-116360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:116352400-116353800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:116352600-116356200	Weak transcription	HSMMtube	muscle
26	chr10:116352600-116360000	Weak transcription	Fetal Intestine Large	intestine
27	chr10:116352600-116367600	Weak transcription	Ovary	ovary
28	chr10:116352800-116353200	Weak transcription	Left Ventricle	heart
29	chr10:116352800-116353600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr10:116352800-116354200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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