Variant report

Variant	rs11049999
Chromosome Location	chr12:29195787-29195788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10743637	0.87[ASN][1000 genomes]
rs10743641	0.83[AFR][1000 genomes]
rs10771470	0.83[AFR][1000 genomes]
rs10771471	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10771477	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1344854	0.80[AFR][1000 genomes]
rs4471475	0.87[ASN][1000 genomes]
rs7955393	0.80[AFR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2758301	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759888	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1802947	chr12:29194445-29197813	Active TSS Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11049999	RP11-996F15.2	cis	lung	GTEx
rs11049999	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29191400-29197200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:29191600-29196000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:29191800-29197000	Enhancers	NHLF	lung
4	chr12:29193200-29196000	Weak transcription	Fetal Stomach	stomach
5	chr12:29194400-29196400	Enhancers	HSMM	muscle
6	chr12:29194400-29197000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:29194400-29198000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:29194600-29196200	Enhancers	NH-A	brain
9	chr12:29195200-29197200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:29195200-29197200	Enhancers	Osteobl	bone
11	chr12:29195400-29197200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:29195400-29198600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:29195600-29196400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr12:29195600-29196400	Enhancers	Fetal Intestine Small	intestine
15	chr12:29195600-29196600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:29195600-29196600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:29195600-29197600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:29195600-29198000	Enhancers	NHDF-Ad	bronchial

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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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