Variant report

Variant	rs2569441
Chromosome Location	chr19:51514622-51514623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10420303	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10426	0.88[YRI][hapmap]
rs1532901	0.86[CEU][hapmap]
rs1654559	0.88[CEU][hapmap]
rs1698	0.80[CEU][hapmap]
rs1701916	0.87[CEU][hapmap]
rs1701921	0.88[CEU][hapmap]
rs1701948	0.96[CEU][hapmap]
rs2075802	0.85[GIH][hapmap]
rs2222554	0.81[CEU][hapmap]
rs2569439	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2569440	0.81[EUR][1000 genomes]
rs2569443	0.84[CEU][hapmap]
rs2569478	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659071	0.88[CEU][hapmap]
rs268899	0.92[CEU][hapmap]
rs2739429	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs906190	0.88[CEU][hapmap]
rs952109	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912291	chr19:51505725-51537682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv579961	chr19:51509726-51516015	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2569441	RPS5	cis	parietal	SCAN
rs2569441	LILRA1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51510200-51517000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:51512000-51514800	Enhancers	HMEC	breast
3	chr19:51513000-51514800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:51513400-51514800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:51513400-51514800	Enhancers	NHEK	skin
6	chr19:51514400-51519000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:51514600-51517200	Weak transcription	Esophagus	oesophagus

Quick Search:

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

what's new

Quick links