Variant report

Variant	rs13078891
Chromosome Location	chr3:111385006-111385007
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	chr3:111295710..111298170-chr3:111384643..111386877,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13086157	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1355767	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1398747	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1553970	0.84[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1606503	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036995	0.92[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2036996	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35957576	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4481128	0.93[TSI][hapmap]
rs4682052	0.92[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682292	0.86[ASN][1000 genomes]
rs4682295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62275506	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs867293	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13078891	PLCXD2	cis	cerebellum	SCAN
rs13078891	ZBED2	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111374000-111385200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:111381000-111385800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111381200-111385600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:111381200-111386000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:111381200-111386000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:111382200-111385800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:111382400-111385800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:111383200-111385600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:111383200-111386000	Weak transcription	Primary B cells from cord blood	blood
10	chr3:111383400-111385800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:111383400-111386000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:111384000-111386200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:111384200-111385800	Genic enhancers	Primary T cells from cord blood	blood
14	chr3:111384200-111386400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:111384400-111386200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:111384400-111389200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:111384400-111389400	Enhancers	NHEK	skin
18	chr3:111384400-111389600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111384600-111385400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:111384600-111385400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:111384600-111385400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:111384600-111385800	Enhancers	Osteobl	bone
23	chr3:111384600-111386000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:111384600-111386200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:111384600-111388000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:111384600-111388400	Enhancers	Fetal Thymus	thymus
27	chr3:111384600-111389400	Enhancers	HMEC	breast
28	chr3:111384800-111385400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:111384800-111385800	Enhancers	HUVEC	blood vessel
30	chr3:111384800-111386400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:111384800-111386400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:111384800-111386400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:111384800-111387000	Enhancers	Placenta	Placenta
34	chr3:111384800-111387800	Weak transcription	NH-A	brain
35	chr3:111384800-111388800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:111384800-111390000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:111385000-111385200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:111385000-111385200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:111385000-111385200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:111385000-111385200	Enhancers	HSMM	muscle
41	chr3:111385000-111386200	Genic enhancers	Dnd41	blood
42	chr3:111385000-111392600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links