Variant report

Variant	rs11745309
Chromosome Location	chr5:52239215-52239216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10471826	0.83[EUR][1000 genomes]
rs1047481	0.83[EUR][1000 genomes]
rs1047482	0.83[EUR][1000 genomes]
rs1047483	0.83[EUR][1000 genomes]
rs1047485	0.83[EUR][1000 genomes]
rs10940282	0.83[EUR][1000 genomes]
rs10940283	0.83[EUR][1000 genomes]
rs10940284	0.82[EUR][1000 genomes]
rs1124141	0.83[EUR][1000 genomes]
rs11748504	0.91[YRI][hapmap]
rs1421942	0.85[EUR][1000 genomes]
rs2193968	0.83[EUR][1000 genomes]
rs3088363	0.83[EUR][1000 genomes]
rs3088364	0.83[EUR][1000 genomes]
rs3088365	0.83[EUR][1000 genomes]
rs3212391	0.85[EUR][1000 genomes]
rs36000043	0.83[EUR][1000 genomes]
rs3764923	0.80[EUR][1000 genomes]
rs6859171	0.81[YRI][hapmap]
rs6869687	0.82[EUR][1000 genomes]
rs6869689	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6890588	0.83[EUR][1000 genomes]
rs6895049	0.83[EUR][1000 genomes]
rs6895250	0.82[EUR][1000 genomes]
rs7703316	0.80[EUR][1000 genomes]
rs9292000	0.83[EUR][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
rs11745309	ITGA2	cis	Artery Tibial	GTEx

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	chr5:52218600-52239400	Weak transcription	Ovary	ovary
7	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
8	chr5:52218800-52240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:52219200-52240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:52219200-52240800	Weak transcription	NHLF	lung
11	chr5:52220000-52243000	Weak transcription	Gastric	stomach
12	chr5:52220400-52239400	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:52221400-52240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:52224000-52239400	Weak transcription	Fetal Stomach	stomach
17	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
18	chr5:52225200-52239800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:52227000-52240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:52228400-52240800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
23	chr5:52232200-52240600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
25	chr5:52235000-52240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52235000-52240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:52235400-52243200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:52236000-52239400	Weak transcription	Fetal Intestine Small	intestine
29	chr5:52236000-52240400	Weak transcription	NHDF-Ad	bronchial
30	chr5:52236000-52240800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:52237000-52240800	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:52237200-52239400	Weak transcription	Aorta	Aorta
33	chr5:52237200-52240000	Weak transcription	Dnd41	blood
34	chr5:52237400-52239400	Weak transcription	Lung	lung
35	chr5:52237400-52240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:52237400-52240800	Weak transcription	Adipose Nuclei	Adipose
37	chr5:52238000-52239400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:52238800-52240200	Strong transcription	Fetal Lung	lung
39	chr5:52238800-52252200	Strong transcription	Liver	Liver
40	chr5:52239000-52240400	Strong transcription	Fetal Intestine Large	intestine
41	chr5:52239200-52239600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:52239200-52240000	Strong transcription	Placenta	Placenta
43	chr5:52239200-52240000	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr5:52239200-52240200	Genic enhancers	Spleen	Spleen

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