Variant report

Variant	rs13074501
Chromosome Location	chr3:146271370-146271371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:146268773..146270653-chr3:146270880..146272451,2	K562	blood:
2	chr3:146271238..146272788-chr3:146273946..146275885,2	K562	blood:
3	chr3:146259917..146263549-chr3:146271246..146274873,4	MCF-7	breast:
4	chr3:146053792..146056507-chr3:146270955..146273271,2	K562	blood:
5	chr3:146245158..146247754-chr3:146270114..146271992,2	K562	blood:
6	chr3:146261061..146263608-chr3:146270616..146272479,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13069082	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs1443827	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1546420	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546421	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579786	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1579787	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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];0.83[MKK][hapmap];0.89[ASN][1000 genomes]
rs343340	0.83[LWK][hapmap]
rs34682680	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35046242	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35416584	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615988	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7639636	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs977757	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977758	0.88[EUR][1000 genomes]
rs977759	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810169	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813199	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs9832220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861142	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs9865918	0.88[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
rs13074501	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146263800-146271800	Weak transcription	K562	blood
2	chr3:146267200-146271600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:146267800-146272000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:146268200-146272200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:146268600-146271600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:146268800-146272400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:146269000-146272000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:146269200-146271400	Weak transcription	Dnd41	blood
9	chr3:146269200-146271800	Weak transcription	A549	lung
10	chr3:146269200-146273200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:146269400-146272000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:146269600-146271600	Weak transcription	GM12878-XiMat	blood
13	chr3:146270000-146284000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:146270200-146274200	Weak transcription	HMEC	breast
15	chr3:146271000-146271400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:146271000-146271800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr3:146271200-146271600	Enhancers	Primary B cells from cord blood	blood
18	chr3:146271200-146272600	Enhancers	Primary monocytes fromperipheralblood	blood

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