Variant report

Variant	rs12518589
Chromosome Location	chr5:178068117-178068118
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	chr5:178054847..178056678-chr5:178067285..178069085,2	K562	blood:
3	chr5:178053270..178056347-chr5:178066420..178069487,3	K562	blood:
4	chr5:178063122..178065248-chr5:178068092..178070072,3	K562	blood:
5	chr5:178052435..178056379-chr5:178060810..178069102,10	MCF-7	breast:
6	chr5:178067993..178069564-chr5:178084194..178086392,2	K562	blood:
7	chr5:178058537..178060660-chr5:178067167..178069118,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10063220	0.91[ASN][1000 genomes]
rs11249553	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11249554	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11249556	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11737903	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11740194	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11746942	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11747742	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12514311	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13155255	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156622	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35460909	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35522922	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36008351	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3925518	0.91[ASN][1000 genomes]
rs4079110	0.89[ASN][1000 genomes]
rs4587090	0.89[ASN][1000 genomes]
rs4976738	0.90[ASN][1000 genomes]
rs4976800	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501721	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs519984	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs530542	0.86[EUR][1000 genomes]
rs574103	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs576097	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs584415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs596780	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs602019	0.83[ASN][1000 genomes]
rs602451	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs643936	0.86[EUR][1000 genomes]
rs649585	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6863876	0.89[ASN][1000 genomes]
rs6865775	0.91[ASN][1000 genomes]
rs6882079	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6883747	0.91[ASN][1000 genomes]
rs6886390	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890632	0.91[ASN][1000 genomes]
rs721144	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702727	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9329045	0.91[ASN][1000 genomes]
rs9329046	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12518589	CLK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178065000-178069600	Weak transcription	Spleen	Spleen
2	chr5:178067000-178068600	Weak transcription	Placenta	Placenta
3	chr5:178067400-178070400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:178067400-178070800	Enhancers	HMEC	breast
5	chr5:178067600-178070200	Enhancers	NHDF-Ad	bronchial
6	chr5:178067600-178070800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:178067600-178072400	Enhancers	Osteobl	bone
8	chr5:178068000-178068400	Weak transcription	NHEK	skin
9	chr5:178068000-178069000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:178068000-178070200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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