Variant report

Variant	rs2141707
Chromosome Location	chr12:76225830-76225831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10879990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12317066	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1275615	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1275616	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7134254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295719	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7296002	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7305444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307780	0.93[ASN][1000 genomes]
rs7957404	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7965922	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7972673	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7977768	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv826440	chr12:76224278-76230703	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2141707	TSPAN8	cis	parietal	SCAN
rs2141707	PMF1	trans	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76220400-76230000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:76221200-76228200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:76221600-76228200	Weak transcription	NHEK	skin
4	chr12:76225000-76226000	Enhancers	Fetal Heart	heart
5	chr12:76225000-76226400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:76225200-76226800	Enhancers	NHLF	lung
7	chr12:76225600-76228400	Weak transcription	HUVEC	blood vessel
8	chr12:76225600-76229800	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:76225600-76230400	Weak transcription	HepG2	liver
10	chr12:76225600-76231400	Weak transcription	NHDF-Ad	bronchial
11	chr12:76225600-76234200	Weak transcription	Fetal Brain Female	brain
12	chr12:76225800-76228200	Weak transcription	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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