Variant report

Variant	rs13156622
Chromosome Location	chr5:178063528-178063529
allele	C/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	chr5:178053909..178055898-chr5:178062249..178064358,2	MCF-7	breast:
3	chr5:178063341..178065728-chr5:178071679..178073201,2	MCF-7	breast:
4	chr5:178052435..178056379-chr5:178060810..178069102,10	MCF-7	breast:
5	chr5:178063122..178065248-chr5:178068092..178070072,3	K562	blood:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10063220	0.89[ASN][1000 genomes]
rs11249553	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11249554	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11249556	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737903	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740194	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11746942	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11747742	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12514311	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518589	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13155255	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35460909	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35522922	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36008351	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3925518	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4079110	0.88[ASN][1000 genomes]
rs4587090	0.88[ASN][1000 genomes]
rs4976738	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4976800	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501721	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs519984	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530542	0.86[EUR][1000 genomes]
rs555417	0.85[JPT][hapmap];0.87[YRI][hapmap]
rs574103	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576097	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs584415	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs596780	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602019	0.84[ASN][1000 genomes]
rs602451	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap]
rs643936	0.86[EUR][1000 genomes]
rs649585	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6863876	0.87[ASN][1000 genomes]
rs6865775	0.89[ASN][1000 genomes]
rs6882079	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6883747	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6886390	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6890632	0.89[ASN][1000 genomes]
rs721144	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7700943	0.81[CEU][hapmap]
rs7702727	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7724406	0.81[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs9329045	0.89[ASN][1000 genomes]
rs9329046	0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13156622	CLK4	cis	normal skin	skin_eQTL
rs13156622	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178059600-178064000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:178062600-178064400	Weak transcription	HepG2	liver
3	chr5:178062800-178064200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:178062800-178067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:178062800-178067600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:178063200-178067400	Weak transcription	HMEC	breast
7	chr5:178063400-178066800	Weak transcription	Placenta	Placenta
8	chr5:178063400-178067400	Weak transcription	NHEK	skin

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