Variant report

Variant	rs10940285
Chromosome Location	chr5:52253394-52253395
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA2-4	chr5:52251187-52255037	NONHSAT101419

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1047481	0.95[LWK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs1047482	0.85[AFR][1000 genomes]
rs1047483	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs1047485	0.85[AFR][1000 genomes]
rs10805444	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940283	0.84[AFR][1000 genomes]
rs10940284	0.87[AFR][1000 genomes]
rs10940286	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940287	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124141	0.86[AFR][1000 genomes]
rs11739193	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740823	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742531	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742558	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743233	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659969	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152074	0.96[EUR][1000 genomes]
rs152091	0.96[EUR][1000 genomes]
rs152092	0.96[EUR][1000 genomes]
rs165981	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs165982	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs181769	0.94[EUR][1000 genomes]
rs2193968	0.95[LWK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs246407	0.96[EUR][1000 genomes]
rs246408	0.96[EUR][1000 genomes]
rs246409	0.96[EUR][1000 genomes]
rs246410	0.96[EUR][1000 genomes]
rs246411	0.96[EUR][1000 genomes]
rs246412	0.95[EUR][1000 genomes]
rs246413	0.95[EUR][1000 genomes]
rs246414	0.95[EUR][1000 genomes]
rs246514	0.96[EUR][1000 genomes]
rs246515	0.91[EUR][1000 genomes]
rs246516	0.89[EUR][1000 genomes]
rs246517	0.95[EUR][1000 genomes]
rs246519	0.94[EUR][1000 genomes]
rs246523	0.92[EUR][1000 genomes]
rs246524	0.94[EUR][1000 genomes]
rs3088363	0.84[AFR][1000 genomes]
rs3088364	0.85[AFR][1000 genomes]
rs3088365	0.95[LWK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs34598281	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764924	0.96[CEU][hapmap]
rs427136	0.88[EUR][1000 genomes]
rs6450100	0.96[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs6869687	0.85[AFR][1000 genomes]
rs6882655	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890588	0.91[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs6895049	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs6895250	0.85[AFR][1000 genomes]
rs7034	0.96[CEU][hapmap]
rs7035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703316	0.85[AFR][1000 genomes]
rs7729947	0.91[AMR][1000 genomes]
rs9686952	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791116	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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
rs10940285	ITGA2	cis	Heart Left Ventricle	GTEx
rs10940285	ITGA2	cis	Artery Tibial	GTEx
rs10940285	PARP8	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
2	chr5:52240000-52253600	Weak transcription	Lung	lung
3	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
4	chr5:52244800-52253600	Weak transcription	Fetal Stomach	stomach
5	chr5:52245200-52253400	Weak transcription	HSMMtube	muscle
6	chr5:52246000-52254400	Weak transcription	Fetal Kidney	kidney
7	chr5:52246200-52254200	Weak transcription	Fetal Lung	lung
8	chr5:52246800-52253600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:52247600-52257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:52250000-52271600	Weak transcription	Aorta	Aorta
11	chr5:52251800-52253600	Enhancers	Fetal Intestine Small	intestine
12	chr5:52251800-52254000	Enhancers	Fetal Intestine Large	intestine
13	chr5:52252000-52253600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:52252000-52253600	Enhancers	Duodenum Mucosa	Duodenum
15	chr5:52252000-52253600	Flanking Active TSS	HepG2	liver
16	chr5:52252200-52253600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:52252400-52253600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:52252600-52253400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:52252600-52253400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:52252600-52253600	Enhancers	A549	lung
21	chr5:52252600-52254000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr5:52252600-52254200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:52252600-52257000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:52252800-52253600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:52252800-52253600	Enhancers	NHEK	skin
26	chr5:52252800-52254400	Weak transcription	Adipose Nuclei	Adipose
27	chr5:52252800-52254600	Weak transcription	Liver	Liver
28	chr5:52252800-52255800	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:52252800-52257000	Weak transcription	Left Ventricle	heart
30	chr5:52252800-52259000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:52253000-52253400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:52253000-52253400	Enhancers	HMEC	breast
33	chr5:52253000-52253600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:52253000-52253600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:52253000-52253600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:52253200-52253400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:52253200-52253400	Enhancers	Fetal Brain Female	brain
38	chr5:52253200-52253600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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