Variant report

Variant	rs11249556
Chromosome Location	chr5:178077667-178077668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10063220	0.82[ASN][1000 genomes]
rs11249553	0.82[EUR][1000 genomes]
rs11249554	0.84[EUR][1000 genomes]
rs11737903	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11740194	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11746942	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11747742	0.96[CEU][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12514311	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12518589	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13155255	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs13156622	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35522922	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36008351	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3925518	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4079110	0.83[ASN][1000 genomes]
rs4587090	0.83[ASN][1000 genomes]
rs4976738	0.81[ASN][1000 genomes]
rs4976800	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs501721	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs555417	0.88[JPT][hapmap]
rs574103	0.80[AFR][1000 genomes]
rs576097	0.82[EUR][1000 genomes]
rs584415	0.80[EUR][1000 genomes]
rs596780	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs602451	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs628857	0.89[CEU][hapmap]
rs649585	0.82[EUR][1000 genomes]
rs6863876	0.84[ASN][1000 genomes]
rs6865775	0.82[ASN][1000 genomes]
rs6882079	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6883747	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6886390	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6890632	0.82[ASN][1000 genomes]
rs7702727	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7732660	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs9329045	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv5155	chr5:178075100-178132799	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11249556	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs11249556	CLK4	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178070200-178078000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:178076000-178077800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:178077400-178077800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:178077400-178078000	Enhancers	Osteobl	bone
5	chr5:178077400-178079200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:178077600-178078200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:178077600-178078400	Enhancers	Muscle Satellite Cultured Cells	--

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