Variant report

Variant	rs2116441
Chromosome Location	chr2:54995746-54995747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1510614	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1813272	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1848924	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1848925	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288682	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288683	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671972	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs980644	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv1844855	chr2:54987215-55012202	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2116441	CCDC85A	cis	cerebellum	SCAN
rs2116441	PTCD3	trans	parietal	SCAN
rs2116441	EML6	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54992200-54998600	Weak transcription	Fetal Brain Female	brain
2	chr2:54993600-54996600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:54994400-54995800	Enhancers	HUVEC	blood vessel
4	chr2:54994600-54996200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:54994800-54995800	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:54994800-54995800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:54994800-54996400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:54995200-54997800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:54995600-54995800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:54995600-54997400	Weak transcription	HSMMtube	muscle
11	chr2:54995600-54997400	Weak transcription	NHEK	skin
12	chr2:54995600-54997600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:54995600-54997600	Weak transcription	HMEC	breast
14	chr2:54995600-54997600	Weak transcription	HSMM	muscle
15	chr2:54995600-54997600	Weak transcription	NH-A	brain
16	chr2:54995600-54997800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:54995600-54997800	Weak transcription	NHDF-Ad	bronchial
18	chr2:54995600-54998400	Weak transcription	Hela-S3	cervix
19	chr2:54995600-54998800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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