Variant report

Variant	rs1085622
Chromosome Location	chr3:120008607-120008608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10049256	0.86[ASN][1000 genomes]
rs1085620	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085624	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934512	0.86[ASN][1000 genomes]
rs10934514	0.83[ASN][1000 genomes]
rs10934515	0.86[ASN][1000 genomes]
rs10934516	0.86[ASN][1000 genomes]
rs10934517	0.86[ASN][1000 genomes]
rs11707711	0.83[ASN][1000 genomes]
rs12152218	0.86[ASN][1000 genomes]
rs13314898	0.95[ASN][1000 genomes]
rs1352458	0.86[ASN][1000 genomes]
rs1388755	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1488761	0.86[ASN][1000 genomes]
rs1488764	0.86[ASN][1000 genomes]
rs1492271	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907681	0.86[ASN][1000 genomes]
rs2035671	0.86[ASN][1000 genomes]
rs2130000	0.86[ASN][1000 genomes]
rs2131174	0.81[ASN][1000 genomes]
rs2171598	0.86[ASN][1000 genomes]
rs2319541	0.86[ASN][1000 genomes]
rs2319542	0.86[ASN][1000 genomes]
rs2319543	0.86[ASN][1000 genomes]
rs2874022	0.81[ASN][1000 genomes]
rs2874023	0.86[ASN][1000 genomes]
rs2943755	0.95[ASN][1000 genomes]
rs2971211	0.95[ASN][1000 genomes]
rs2971213	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4263318	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314205	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676804	0.83[ASN][1000 genomes]
rs4676809	0.86[ASN][1000 genomes]
rs4676822	0.86[ASN][1000 genomes]
rs4676832	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438567	0.86[ASN][1000 genomes]
rs6764549	0.86[ASN][1000 genomes]
rs6772226	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775625	0.81[ASN][1000 genomes]
rs6776122	0.86[ASN][1000 genomes]
rs6777971	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6787458	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803611	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805050	0.86[ASN][1000 genomes]
rs7637828	0.86[ASN][1000 genomes]
rs7641838	0.86[ASN][1000 genomes]
rs7642171	0.86[ASN][1000 genomes]
rs7653263	0.86[ASN][1000 genomes]
rs7653396	0.86[ASN][1000 genomes]
rs787185	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787198	0.89[ASN][1000 genomes]
rs787211	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796824	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813697	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814182	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902790	0.86[ASN][1000 genomes]
rs902791	0.86[ASN][1000 genomes]
rs902792	0.86[ASN][1000 genomes]
rs902794	0.86[ASN][1000 genomes]
rs923726	0.86[ASN][1000 genomes]
rs923727	0.86[ASN][1000 genomes]
rs923728	0.86[ASN][1000 genomes]
rs9289142	0.86[ASN][1000 genomes]
rs9289143	0.86[ASN][1000 genomes]
rs979682	0.86[ASN][1000 genomes]
rs9811483	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9813834	0.86[ASN][1000 genomes]
rs9841122	0.86[ASN][1000 genomes]
rs9842302	0.86[ASN][1000 genomes]
rs9849023	0.81[ASN][1000 genomes]
rs9853082	0.86[ASN][1000 genomes]
rs9857123	0.86[ASN][1000 genomes]
rs9858566	0.86[ASN][1000 genomes]
rs9868058	0.83[ASN][1000 genomes]
rs9868312	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1085622	PLA1A	cis	brain	BrainEAC

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120004400-120010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:120008600-120008800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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