Variant report

Variant	rs1550396
Chromosome Location	chr2:12172450-12172451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10929781	0.81[EUR][1000 genomes]
rs12471493	0.81[EUR][1000 genomes]
rs12692452	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987412	0.81[EUR][1000 genomes]
rs13002231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007105	0.99[EUR][1000 genomes]
rs1550395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165219	0.81[EUR][1000 genomes]
rs2165220	0.81[EUR][1000 genomes]
rs6761070	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7560369	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7584367	0.81[EUR][1000 genomes]
rs7585074	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12171200-12178000	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:12171400-12173600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:12171600-12172800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:12171600-12173400	Flanking Active TSS	GM12878-XiMat	blood
5	chr2:12172000-12173400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:12172200-12172800	Enhancers	Ovary	ovary
7	chr2:12172200-12174000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:12172200-12174000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:12172200-12174200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:12172200-12176000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:12172400-12172600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:12172400-12173000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:12172400-12173800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:12172400-12174400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:12172400-12175800	Weak transcription	K562	blood

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

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