Variant report

Variant	rs4976738
Chromosome Location	chr5:178071546-178071547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178063343..178066239-chr5:178068092..178071855,3	K562	blood:
2	chr5:178051814..178054054-chr5:178071532..178073696,2	MCF-7	breast:
3	chr5:178066224..178067875-chr5:178070562..178072155,2	K562	blood:
4	chr5:178053031..178055568-chr5:178069602..178071644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10063148	0.96[CEU][hapmap]
rs10063220	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10464070	0.82[CEU][hapmap]
rs10479500	0.88[CEU][hapmap]
rs11249556	0.81[ASN][1000 genomes]
rs11737903	0.83[ASN][1000 genomes]
rs11740194	0.83[ASN][1000 genomes]
rs11746942	0.83[ASN][1000 genomes]
rs11747742	0.83[ASN][1000 genomes]
rs12188543	0.85[CEU][hapmap]
rs12189095	0.85[CEU][hapmap]
rs12514311	0.84[ASN][1000 genomes]
rs12518589	0.90[ASN][1000 genomes]
rs13156622	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs35522922	0.89[ASN][1000 genomes]
rs36008351	0.90[ASN][1000 genomes]
rs3925517	0.85[CEU][hapmap]
rs3925518	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4079110	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587090	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976800	0.81[ASN][1000 genomes]
rs530542	0.81[ASN][1000 genomes]
rs628857	0.83[JPT][hapmap]
rs643936	0.82[ASN][1000 genomes]
rs6863876	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865775	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6882079	0.83[ASN][1000 genomes]
rs6883747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6890632	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7702727	0.83[ASN][1000 genomes]
rs9329045	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9329046	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4976738	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178067600-178072400	Enhancers	Osteobl	bone
2	chr5:178070200-178071600	Weak transcription	NHDF-Ad	bronchial
3	chr5:178070200-178071600	Weak transcription	NHEK	skin
4	chr5:178070200-178072000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:178070200-178072000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:178070200-178072200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:178070200-178078000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:178070400-178071600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:178070400-178071800	Weak transcription	Hela-S3	cervix
10	chr5:178070600-178071600	Weak transcription	HUVEC	blood vessel
11	chr5:178070600-178071600	Weak transcription	NH-A	brain
12	chr5:178071200-178072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:178071200-178072600	Enhancers	HMEC	breast
14	chr5:178071400-178071600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:178071400-178071600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr5:178071400-178072600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:178071400-178072600	Enhancers	Monocytes-CD14+_RO01746	blood

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