Variant report

Variant	rs6861460
Chromosome Location	chr5:52254346-52254347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs26679	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs26681	0.87[EUR][1000 genomes]
rs28095	0.87[EUR][1000 genomes]
rs33445	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs33446	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs33447	0.90[EUR][1000 genomes]
rs33448	0.89[EUR][1000 genomes]
rs42776	0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6861460	ITGA2	cis	Adipose Subcutaneous	GTEx
rs6861460	ITGA2	cis	parietal	SCAN
rs6861460	PARP8	cis	cerebellum	SCAN
rs6861460	ITGA2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

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

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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