Variant report

Variant	rs977757
Chromosome Location	chr3:146276712-146276713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13069082	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs13074501	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443827	0.96[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1546420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546421	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579786	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1579787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083866	0.97[ASN][1000 genomes]
rs2587021	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2738921	0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs34682680	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35046242	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35416584	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615988	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs7639636	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs977758	0.90[EUR][1000 genomes]
rs977759	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810169	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813199	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9832220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861142	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9865918	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
2	nsv432489	chr3:146271370-146323969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs977757	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146270000-146284000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:146275400-146277400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:146275400-146277400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:146275600-146277600	Enhancers	Primary B cells from cord blood	blood
5	chr3:146275800-146286200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:146276400-146276800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:146276600-146276800	Enhancers	GM12878-XiMat	blood
8	chr3:146276600-146277000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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