Variant report

Variant	rs17143900
Chromosome Location	chr5:117568527-117568528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10519541	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11739862	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11748941	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1479214	0.95[ASN][1000 genomes]
rs1479219	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479220	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17143903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17143923	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34339507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41456648	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5004250	0.82[ASN][1000 genomes]
rs56090853	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56118268	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57486817	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58867284	0.95[ASN][1000 genomes]
rs6877628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7341174	0.95[ASN][1000 genomes]
rs7447026	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327069	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

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	nsv1027428	chr5:117072745-118036353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537877	chr5:117072745-118036353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1067621	chr5:117102544-118036352	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv531292	chr5:117102544-118036352	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1021879	chr5:117386077-117570453	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2422395	chr5:117442806-117887910	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv882762	chr5:117499480-117706786	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	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
rs17143900	ZNF474	cis	parietal	SCAN
rs17143900	IL10RA	trans	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:117567200-117568800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:117567200-117569000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:117568400-117570400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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