Variant report

Variant	rs11711599
Chromosome Location	chr3:136698509-136698510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:136698444-136698856	Hela-S3	cervix:	n/a	chr3:136698633-136698642 chr3:136698640-136698648
2	RFX5	chr3:136698452-136698846	HepG2	liver:	n/a	chr3:136698633-136698642 chr3:136698640-136698648
3	RCOR1	chr3:136698179-136699079	IMR90	lung:	n/a	n/a
4	RFX5	chr3:136698302-136698938	SK-N-SH	brain:	n/a	chr3:136698633-136698642 chr3:136698640-136698648
5	RFX5	chr3:136698119-136698996	IMR90	lung:	n/a	chr3:136698633-136698642 chr3:136698640-136698648

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136693279..136695517-chr3:136697390..136699263,2	K562	blood:

Variant related genes	Relation type
IL20RB	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs12054220	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629000	1.00[CHB][hapmap]
rs13095028	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13095034	0.87[ASN][1000 genomes]
rs1385306	0.82[ASN][1000 genomes]
rs1406539	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1620455	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654900	0.82[ASN][1000 genomes]
rs1654901	0.82[ASN][1000 genomes]
rs1654924	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1682339	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1682361	0.82[ASN][1000 genomes]
rs1682362	0.82[ASN][1000 genomes]
rs1682363	0.82[ASN][1000 genomes]
rs1682364	0.82[ASN][1000 genomes]
rs1682365	0.82[ASN][1000 genomes]
rs1682366	0.82[ASN][1000 genomes]
rs16844241	1.00[CHB][hapmap]
rs168635	0.87[LWK][hapmap]
rs171519	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181732	0.82[ASN][1000 genomes]
rs183120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117008	0.83[ASN][1000 genomes]
rs2344092	0.84[ASN][1000 genomes]
rs361227	0.82[ASN][1000 genomes]
rs361228	0.82[ASN][1000 genomes]
rs361229	0.82[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs361234	0.85[ASN][1000 genomes]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs361238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361239	0.82[LWK][hapmap]
rs361240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361243	0.81[LWK][hapmap]
rs361249	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678275	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678447	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55781515	0.82[ASN][1000 genomes]
rs71620537	0.87[ASN][1000 genomes]
rs747842	0.85[LWK][hapmap]
rs75977	0.82[LWK][hapmap]
rs7610507	1.00[CHB][hapmap]
rs7631541	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs835627	0.82[ASN][1000 genomes]
rs835629	0.82[ASN][1000 genomes]
rs835630	0.82[ASN][1000 genomes]
rs835631	0.82[ASN][1000 genomes]
rs835636	1.00[CHD][hapmap]
rs835637	1.00[CHD][hapmap]
rs835638	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9681468	0.81[ASN][1000 genomes]
rs9682783	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs9845460	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9850024	0.82[ASN][1000 genomes]
rs9854795	0.82[ASN][1000 genomes]
rs9874615	0.82[ASN][1000 genomes]
rs9875855	0.87[ASN][1000 genomes]
rs999038	0.82[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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11711599	PCCB	cis	cerebellum	SCAN
rs11711599	IL20RB	cis	Skin Sun Exposed Lower leg	GTEx
rs11711599	SPSB4	cis	cerebellum	SCAN
rs11711599	PPP2R3A	cis	parietal	SCAN
rs11711599	PCCB	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136694800-136699200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:136695400-136700600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:136695400-136703600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:136695400-136706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:136695600-136700400	Enhancers	Fetal Thymus	thymus
6	chr3:136697200-136698800	Enhancers	Dnd41	blood
7	chr3:136698000-136698800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:136698000-136698800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:136698000-136698800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:136698000-136699000	Genic enhancers	NHEK	skin
11	chr3:136698200-136698800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:136698200-136698800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:136698200-136698800	Enhancers	Esophagus	oesophagus
14	chr3:136698200-136698800	Enhancers	Hela-S3	cervix
15	chr3:136698200-136698800	Enhancers	HMEC	breast
16	chr3:136698200-136698800	Enhancers	NHDF-Ad	bronchial
17	chr3:136698400-136698600	Flanking Active TSS	Thymus	Thymus
18	chr3:136698400-136698800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:136698400-136703600	Weak transcription	Pancreas	Pancrea

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