Variant report

Variant	rs880292
Chromosome Location	chr2:46908796-46908797
allele	G/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:16)

rs_ID	r²[population]
rs1004147	0.94[EUR][1000 genomes]
rs10178013	0.94[EUR][1000 genomes]
rs1319499	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs13425512	0.91[EUR][1000 genomes]
rs1456017	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466268	0.94[EUR][1000 genomes]
rs1563401	0.94[EUR][1000 genomes]
rs1563407	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1902321	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902322	0.93[ASN][1000 genomes]
rs4355163	0.98[ASN][1000 genomes]
rs4952841	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62136934	0.95[ASN][1000 genomes]
rs6713768	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6734725	0.88[ASN][1000 genomes]
rs897532	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
7	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs880292	C2orf61	cis	cerebellum	SCAN
rs880292	CCL13	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46902600-46909600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:46905600-46909600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:46906000-46911400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:46907200-46908800	Enhancers	GM12878-XiMat	blood
5	chr2:46907200-46909400	Enhancers	Primary B cells from cord blood	blood
6	chr2:46907400-46910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:46907600-46911200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:46907600-46911400	Weak transcription	Osteobl	bone
9	chr2:46907800-46911400	Weak transcription	NHDF-Ad	bronchial
10	chr2:46907800-46911800	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:46908200-46908800	Enhancers	Left Ventricle	heart
12	chr2:46908400-46911200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:46908400-46911400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:46908400-46912400	Weak transcription	NHLF	lung
15	chr2:46908600-46908800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:46908600-46909800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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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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