Variant report

Variant	rs866839
Chromosome Location	chr12:44446985-44446986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10748390	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17554795	1.00[LWK][hapmap]
rs2407790	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs842206	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[AFR][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	nsv832390	chr12:44318071-44512114	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1041188	chr12:44331098-44528712	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832391	chr12:44394137-44552555	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs866839	TMEM117	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44423400-44447000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:44438400-44449000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:44439200-44464400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:44445800-44448400	Enhancers	Hela-S3	cervix
5	chr12:44446400-44447000	Enhancers	Gastric	stomach
6	chr12:44446400-44447400	Enhancers	Stomach Mucosa	stomach
7	chr12:44446400-44447600	Enhancers	Duodenum Mucosa	Duodenum
8	chr12:44446400-44447600	Enhancers	Small Intestine	intestine
9	chr12:44446400-44448000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:44446400-44448200	Enhancers	Adipose Nuclei	Adipose
11	chr12:44446800-44447800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:44446800-44448000	Enhancers	HMEC	breast
13	chr12:44446800-44448200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:44446800-44448400	Enhancers	NHEK	skin

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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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