Variant report

Variant	rs10052477
Chromosome Location	chr5:1637461-1637462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:52596128..52598397-chr5:1635134..1637588,2	MCF-7	breast:
2	chr5:1632420..1636449-chr5:1636560..1641821,6	MCF-7	breast:
3	chr5:1637235..1639210-chr5:1639365..1642347,2	K562	blood:
4	chr5:1632750..1636103-chr5:1636749..1640092,3	K562	blood:

Variant related genes	Relation type
ENSG00000188002	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10040389	0.85[ASN][1000 genomes]
rs10061756	0.94[ASN][1000 genomes]
rs10062417	0.81[ASN][1000 genomes]
rs10062809	0.85[ASN][1000 genomes]
rs10062957	0.85[ASN][1000 genomes]
rs10064943	0.84[ASN][1000 genomes]
rs10074018	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10474721	0.85[ASN][1000 genomes]
rs10475075	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475076	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10475077	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1048186	0.81[ASN][1000 genomes]
rs11958585	0.81[ASN][1000 genomes]
rs12153695	0.91[CEU][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs41408448	0.95[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55854954	0.84[ASN][1000 genomes]
rs58775025	0.81[ASN][1000 genomes]
rs6554915	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap]
rs6897545	0.84[ASN][1000 genomes]
rs72719219	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72719222	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705049	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7710273	0.81[ASN][1000 genomes]
rs7734561	0.89[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9312909	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10052477	PDCD6	cis	uninvolved skin	skin_eQTL
rs10052477	RP11-43F13.1	cis	Whole Blood	GTEx
rs10052477	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs10052477	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs10052477	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs10052477	CTD-2012J19.1	cis	Thyroid	GTEx
rs10052477	CTD-2012J19.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10052477	RP11-43F13.1	cis	Adipose Subcutaneous	GTEx
rs10052477	PDCD6	cis	lesional skin	skin_eQTL
rs10052477	CTD-2012J19.1	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1635200-1640000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:1635400-1638000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:1637200-1638200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:1637400-1638000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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