Variant report

Variant	rs2407790
Chromosome Location	chr12:44431493-44431494
allele	A/G
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	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492310	0.89[LWK][hapmap];1.00[MKK][hapmap]
rs842209	0.85[MKK][hapmap]
rs866839	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]

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
rs2407790	TMEM117	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44390800-44439200	Weak transcription	Esophagus	oesophagus
2	chr12:44402000-44432200	Weak transcription	Aorta	Aorta
3	chr12:44422200-44437800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:44423200-44434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:44423400-44447000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:44427000-44432200	Weak transcription	Left Ventricle	heart
7	chr12:44429000-44446800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:44430200-44440400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:44430400-44439600	Weak transcription	Fetal Intestine Large	intestine
10	chr12:44430800-44432200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:44430800-44432400	Enhancers	Pancreas	Pancrea
12	chr12:44430800-44432600	Strong transcription	Fetal Intestine Small	intestine
13	chr12:44431000-44437200	Weak transcription	Fetal Stomach	stomach
14	chr12:44431400-44431800	Enhancers	Right Ventricle	heart
15	chr12:44431400-44432000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:44431400-44446400	Weak transcription	Gastric	stomach

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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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