Variant report

Variant	rs10513004
Chromosome Location	chr5:52235225-52235226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10940280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738606	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739571	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742694	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742813	0.88[EUR][1000 genomes]
rs11748504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749081	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12186544	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13156420	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13165509	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13179969	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180488	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421943	0.87[EUR][1000 genomes]
rs3212383	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs3212656	0.84[EUR][1000 genomes]
rs34288275	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34352729	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34512129	0.87[EUR][1000 genomes]
rs34865297	0.86[EUR][1000 genomes]
rs35597318	0.87[EUR][1000 genomes]
rs35657730	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35862618	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35926366	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865755	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs6859171	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702766	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7713782	0.84[EUR][1000 genomes]
rs9791046	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10513004	ITGA2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52206400-52240800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:52211400-52239400	Weak transcription	Right Ventricle	heart
4	chr5:52211400-52240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:52211600-52244400	Weak transcription	HepG2	liver
6	chr5:52212200-52237400	Strong transcription	Liver	Liver
7	chr5:52218600-52237000	Weak transcription	Psoas Muscle	Psoas
8	chr5:52218600-52239400	Weak transcription	Ovary	ovary
9	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
10	chr5:52218800-52240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:52219200-52240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:52219200-52240800	Weak transcription	NHLF	lung
13	chr5:52220000-52243000	Weak transcription	Gastric	stomach
14	chr5:52220400-52239400	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:52220600-52235600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:52220600-52236600	Weak transcription	Lung	lung
17	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:52221400-52240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:52224000-52236800	Weak transcription	Aorta	Aorta
21	chr5:52224000-52239400	Weak transcription	Fetal Stomach	stomach
22	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
23	chr5:52225200-52239800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:52227000-52240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:52228400-52240800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:52228600-52235400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr5:52229200-52236600	Weak transcription	Dnd41	blood
29	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
30	chr5:52232200-52237000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52232200-52237400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr5:52232200-52240600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:52232400-52237400	Strong transcription	Adipose Nuclei	Adipose
34	chr5:52232600-52239200	Weak transcription	Spleen	Spleen
35	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
36	chr5:52234000-52235400	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:52234600-52236200	Strong transcription	Placenta	Placenta
38	chr5:52234800-52237400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:52234800-52238000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:52235000-52240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:52235000-52240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:52235200-52236000	Enhancers	Fetal Intestine Large	intestine
43	chr5:52235200-52236000	Strong transcription	NHDF-Ad	bronchial
44	chr5:52235200-52236200	Strong transcription	Fetal Lung	lung

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