Variant report

Variant	rs12659969
Chromosome Location	chr5:52254022-52254023
allele	C/T
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: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1047481	0.84[CEU][hapmap]
rs1047483	0.85[CEU][hapmap]
rs10805444	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940285	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940286	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940287	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11739193	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740823	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742531	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742558	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743233	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152074	0.96[EUR][1000 genomes]
rs152091	0.96[EUR][1000 genomes]
rs152092	0.96[EUR][1000 genomes]
rs165981	0.89[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	0.84[CEU][hapmap]
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]
rs3088365	0.84[CEU][hapmap]
rs34598281	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764924	0.81[CEU][hapmap]
rs427136	0.88[EUR][1000 genomes]
rs6450100	0.83[CEU][hapmap]
rs6882655	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895049	0.85[CEU][hapmap]
rs7034	0.81[CEU][hapmap]
rs7035	0.87[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7729947	0.87[AMR][1000 genomes]
rs9686952	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791116	0.94[AFR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12659969	ITGA2	cis	Artery Tibial	GTEx
rs12659969	ITGA2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52246000-52254400	Weak transcription	Fetal Kidney	kidney
2	chr5:52246200-52254200	Weak transcription	Fetal Lung	lung
3	chr5:52247600-52257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52250000-52271600	Weak transcription	Aorta	Aorta
5	chr5:52252600-52254200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:52252600-52257000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:52252800-52254400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:52252800-52254600	Weak transcription	Liver	Liver
9	chr5:52252800-52255800	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:52252800-52257000	Weak transcription	Left Ventricle	heart
11	chr5:52252800-52259000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:52253400-52256800	Weak transcription	HMEC	breast
13	chr5:52253600-52255000	Enhancers	HepG2	liver
14	chr5:52253600-52256600	Weak transcription	NHEK	skin
15	chr5:52253600-52256800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:52253600-52257000	Weak transcription	Spleen	Spleen
17	chr5:52253600-52257200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:52253600-52257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:52254000-52254200	Enhancers	Fetal Brain Female	brain

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