Variant report

Variant	rs12324870
Chromosome Location	chr15:78995801-78995802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12901241	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12901331	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12905273	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12905641	0.82[EUR][1000 genomes]
rs28444683	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34067845	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34099810	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34275594	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34422348	0.85[AMR][1000 genomes]
rs34550457	0.82[AMR][1000 genomes]
rs34694149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35701817	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35704045	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58526289	0.82[AMR][1000 genomes]
rs61630816	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62010555	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7169223	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7178007	0.85[AMR][1000 genomes];0.81[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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12324870	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs12324870	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78988600-79001600	Weak transcription	Pancreas	Pancrea
2	chr15:78994400-78996200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:78995400-78996400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:78995400-78996800	Enhancers	Thymus	Thymus
5	chr15:78995400-78997000	Enhancers	Fetal Thymus	thymus
6	chr15:78995600-78996200	Weak transcription	Esophagus	oesophagus
7	chr15:78995800-78996200	Enhancers	NHEK	skin

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Input of quick search could be:

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

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