Variant report

Variant	rs809792
Chromosome Location	chr3:120029647-120029648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10048964	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10049256	1.00[JPT][hapmap]
rs1085614	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085616	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085617	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934512	1.00[JPT][hapmap]
rs10934517	1.00[JPT][hapmap]
rs1147681	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147688	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147689	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147690	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11914405	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11928731	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12152218	1.00[JPT][hapmap]
rs13318758	0.89[AMR][1000 genomes]
rs13318838	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327125	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1488764	1.00[JPT][hapmap]
rs1492271	1.00[JPT][hapmap]
rs1625178	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1700	0.92[GIH][hapmap]
rs1716855	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716856	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1733326	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1733328	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1907681	1.00[JPT][hapmap]
rs2035671	1.00[JPT][hapmap]
rs2130000	1.00[JPT][hapmap]
rs2319541	1.00[JPT][hapmap]
rs2319543	1.00[JPT][hapmap]
rs2638597	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28535957	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2874022	1.00[JPT][hapmap]
rs2874023	1.00[JPT][hapmap]
rs28826066	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2971211	1.00[JPT][hapmap]
rs4488869	1.00[JPT][hapmap]
rs4676822	1.00[JPT][hapmap]
rs6438559	1.00[JPT][hapmap]
rs6438564	1.00[JPT][hapmap]
rs6438567	1.00[JPT][hapmap]
rs6764516	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6764549	1.00[JPT][hapmap]
rs6767308	0.92[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6769988	1.00[JPT][hapmap]
rs6776122	1.00[JPT][hapmap]
rs6777979	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6794478	1.00[JPT][hapmap]
rs6803611	1.00[JPT][hapmap]
rs6808913	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7653263	1.00[JPT][hapmap]
rs7653396	1.00[JPT][hapmap]
rs787186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787187	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787189	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787190	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787192	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787193	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787198	1.00[JPT][hapmap]
rs787200	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787205	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs787206	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787207	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787208	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs902790	1.00[JPT][hapmap]
rs902791	1.00[JPT][hapmap]
rs902794	1.00[JPT][hapmap]
rs902795	1.00[JPT][hapmap]
rs923726	1.00[JPT][hapmap]
rs923727	1.00[JPT][hapmap]
rs923728	1.00[JPT][hapmap]
rs923729	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9289143	1.00[JPT][hapmap]
rs9289145	1.00[JPT][hapmap]
rs951658	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs979682	1.00[JPT][hapmap]
rs9810784	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9813834	1.00[JPT][hapmap]
rs9822636	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9822759	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9841122	1.00[JPT][hapmap]
rs9841303	1.00[JPT][hapmap]
rs9842302	1.00[JPT][hapmap]
rs9851711	0.89[AMR][1000 genomes]
rs9853082	1.00[JPT][hapmap]
rs9856670	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9876547	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs809792	PARP15	cis	cerebellum	SCAN
rs809792	B4GALT4	cis	parietal	SCAN
rs809792	GSK3B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:120024600-120032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
5	chr3:120026600-120030600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:120026800-120030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:120026800-120032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:120026800-120032600	Weak transcription	Pancreas	Pancrea
11	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
13	chr3:120027800-120030800	Weak transcription	Fetal Stomach	stomach
14	chr3:120028200-120031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:120029400-120030400	Enhancers	NHEK	skin
16	chr3:120029600-120030000	Enhancers	HMEC	breast
17	chr3:120029600-120032600	Weak transcription	Primary T cells from cord blood	blood

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