Variant report

Variant	rs1550398
Chromosome Location	chr2:12143553-12143554
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10202517	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210269	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929775	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550399	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2380405	0.81[ASN][1000 genomes]
rs4669793	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6432249	0.81[ASN][1000 genomes]
rs6432250	0.81[ASN][1000 genomes]
rs6754671	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6761070	1.00[CEU][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751579	0.94[CHB][hapmap]
rs7560369	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs7563182	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12137200-12148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:12139000-12144800	Weak transcription	Primary T cells from cord blood	blood
3	chr2:12139000-12145200	Weak transcription	HUVEC	blood vessel
4	chr2:12139200-12146200	Weak transcription	NHLF	lung
5	chr2:12139600-12146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:12140200-12145000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:12141400-12147200	Weak transcription	K562	blood
8	chr2:12142400-12145600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:12143000-12143600	ZNF genes & repeats	GM12878-XiMat	blood
10	chr2:12143200-12143800	Enhancers	Aorta	Aorta

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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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