Variant report

Variant	rs3740029
Chromosome Location	chr10:91215809-91215810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11203135	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11203136	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11593758	0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11594380	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11596684	0.82[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11816805	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs17121936	0.83[LWK][hapmap]
rs17122097	0.84[CHB][hapmap]
rs17122257	0.84[CHB][hapmap]
rs17122305	0.84[CHB][hapmap]
rs17387244	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59542683	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3740029	TNKS2	cis	cerebellum	SCAN
rs3740029	ACTA2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91179600-91225600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:91198800-91223600	Weak transcription	Left Ventricle	heart
3	chr10:91212000-91216600	Weak transcription	HUVEC	blood vessel
4	chr10:91213000-91217800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:91214000-91223600	Weak transcription	Pancreas	Pancrea
6	chr10:91214200-91223400	Weak transcription	Placenta	Placenta
7	chr10:91214600-91216000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:91214800-91216000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:91214800-91216000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:91214800-91216200	Enhancers	NHEK	skin
11	chr10:91215000-91217800	Weak transcription	HSMMtube	muscle
12	chr10:91215600-91216000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:91215800-91217600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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