Variant report

Variant	rs7613909
Chromosome Location	chr3:144308606-144308607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1007564	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1007566	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1036439	0.86[JPT][hapmap]
rs11714177	0.83[EUR][1000 genomes]
rs11718059	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1405596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405597	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1657010	0.86[ASN][1000 genomes]
rs2575191	0.81[ASN][1000 genomes]
rs2717391	0.93[EUR][1000 genomes]
rs2717393	0.94[EUR][1000 genomes]
rs28847402	0.97[EUR][1000 genomes]
rs34130084	0.86[ASN][1000 genomes]
rs4388021	0.86[JPT][hapmap]
rs4681378	0.97[EUR][1000 genomes]
rs6440260	0.96[ASN][1000 genomes]
rs73871240	0.80[ASN][1000 genomes]
rs73871243	0.80[ASN][1000 genomes]
rs73871244	0.80[ASN][1000 genomes]
rs73871245	0.80[ASN][1000 genomes]
rs73871248	0.80[ASN][1000 genomes]
rs73871252	0.80[ASN][1000 genomes]
rs9289678	0.96[EUR][1000 genomes]
rs9817588	0.94[EUR][1000 genomes]
rs9840395	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs9856190	0.96[ASN][1000 genomes]
rs9866442	0.95[JPT][hapmap]
rs9878902	0.90[JPT][hapmap]

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	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3379740	chr3:144225847-144433818	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010388	chr3:144236022-144326640	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2757895	chr3:144236202-144391387	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2759185	chr3:144236202-144391387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013350	chr3:144239415-144326640	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv536754	chr3:144239415-144326640	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv877572	chr3:144244265-144312402	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv877573	chr3:144265840-144323993	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7613909	PLSCR1	cis	cerebellum	SCAN
rs7613909	SR140	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144305600-144309400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:144305600-144312600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:144305800-144309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:144307600-144310000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:144308600-144309600	Enhancers	HUVEC	blood vessel
6	chr3:144308600-144310800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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