Variant report

Variant	rs1047483
Chromosome Location	chr5:52249612-52249613
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10471826	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054085	0.82[EUR][1000 genomes]
rs10940281	0.83[CHB][hapmap]
rs10940282	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940284	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940285	0.85[AFR][1000 genomes]
rs1124141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745309	0.83[EUR][1000 genomes]
rs1421927	0.83[CHB][hapmap]
rs1421928	0.80[CHB][hapmap]
rs2193968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2406371	0.83[CHB][hapmap]
rs26682	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs3088363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35235	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs36000043	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764923	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869689	0.82[EUR][1000 genomes]
rs6888620	0.80[CHB][hapmap]
rs6890588	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs7703316	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292000	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1047483	ITGA1	cis	Thyroid	GTEx
rs1047483	ITGA2	cis	Artery Tibial	GTEx
rs1047483	ITGA2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
5	chr5:52238800-52252200	Strong transcription	Liver	Liver
6	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
7	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
8	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
9	chr5:52240000-52253600	Weak transcription	Lung	lung
10	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
11	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
12	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
13	chr5:52241200-52252000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:52243400-52252600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:52244800-52250800	Weak transcription	HepG2	liver
16	chr5:52244800-52253600	Weak transcription	Fetal Stomach	stomach
17	chr5:52245000-52251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:52245200-52249800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:52245200-52253400	Weak transcription	HSMMtube	muscle
20	chr5:52245400-52251000	Weak transcription	NHDF-Ad	bronchial
21	chr5:52245600-52252600	Weak transcription	Dnd41	blood
22	chr5:52245800-52251600	Weak transcription	Placenta	Placenta
23	chr5:52245800-52253000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:52246000-52254400	Weak transcription	Fetal Kidney	kidney
25	chr5:52246200-52251800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:52246200-52254200	Weak transcription	Fetal Lung	lung
27	chr5:52246400-52249800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:52246800-52253600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:52247000-52253000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr5:52247600-52252800	Weak transcription	NHEK	skin
31	chr5:52247600-52253000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:52247600-52253000	Weak transcription	HMEC	breast
33	chr5:52247600-52257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:52248200-52252600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:52248600-52252800	Strong transcription	Adipose Nuclei	Adipose
36	chr5:52249000-52250400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:52249000-52251200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:52249000-52252800	Strong transcription	Colon Smooth Muscle	Colon
39	chr5:52249600-52249800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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