Variant report

Variant	rs9876886
Chromosome Location	chr3:146267662-146267663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146261118..146264072-chr3:146264096..146268231,4	K562	blood:
2	chr3:146262497..146265789-chr3:146267406..146270879,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1057481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1061307	0.89[CHB][hapmap]
rs1079369	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13080178	0.89[CHB][hapmap]
rs13099587	0.89[ASW][hapmap];0.89[CHB][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs1373246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1443827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16858420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882971	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1882972	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1882973	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1882974	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1997601	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997604	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs2120381	1.00[CEU][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2165948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587007	0.92[ASN][1000 genomes]
rs2587008	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2587009	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2587010	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587012	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587013	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587014	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587015	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587016	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587018	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587021	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs2587023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2587024	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2609858	0.99[ASN][1000 genomes]
rs2609860	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609861	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609862	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2609864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2609865	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2609866	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2609867	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688688	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2738905	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2738906	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2738907	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2738910	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738911	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2738912	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2738915	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2738916	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738918	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738920	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738921	0.82[JPT][hapmap]
rs2738923	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35214899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35309521	0.85[ASN][1000 genomes]
rs3773510	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67703040	0.93[ASN][1000 genomes]
rs6799809	0.89[CHB][hapmap]
rs7615988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7625713	0.89[CHB][hapmap]
rs9289722	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs977758	0.95[ASN][1000 genomes]
rs9850802	0.89[CHB][hapmap]
rs9861142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9865918	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9876886	PLSCR1	cis	parietal	SCAN
rs9876886	PLSCR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146262800-146268600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:146263000-146267800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:146263200-146267800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:146263200-146268000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:146263200-146268000	Weak transcription	Osteobl	bone
6	chr3:146263200-146268200	Weak transcription	A549	lung
7	chr3:146263200-146268800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:146263200-146268800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:146263200-146270800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:146263400-146267800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:146263400-146267800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:146263400-146267800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:146263400-146267800	Weak transcription	NHDF-Ad	bronchial
14	chr3:146263400-146268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:146263800-146267800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:146263800-146267800	Weak transcription	NHLF	lung
17	chr3:146263800-146271800	Weak transcription	K562	blood
18	chr3:146265000-146267800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:146265000-146268600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:146265200-146268000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:146265600-146268000	Weak transcription	HMEC	breast
22	chr3:146265600-146269400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:146267000-146269000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:146267000-146269200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:146267000-146269200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:146267200-146271600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:146267400-146267800	Enhancers	Dnd41	blood
28	chr3:146267400-146267800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr3:146267400-146268000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:146267400-146268200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:146267400-146268600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:146267600-146267800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:146267600-146267800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:146267600-146267800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:146267600-146267800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:146267600-146267800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:146267600-146267800	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:146267600-146268000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:146267600-146268000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:146267600-146268200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:146267600-146268200	Enhancers	Primary B cells from cord blood	blood
42	chr3:146267600-146268200	Enhancers	Liver	Liver
43	chr3:146267600-146268200	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:146267600-146268200	Active TSS	Ovary	ovary
45	chr3:146267600-146268600	Active TSS	Colon Smooth Muscle	Colon
46	chr3:146267600-146269400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr3:146267600-146269600	Enhancers	GM12878-XiMat	blood
48	chr3:146267600-146270200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr3:146267600-146270200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:146267600-146270200	Enhancers	NHEK	skin

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