Variant report

Variant	rs13095028
Chromosome Location	chr3:136730155-136730156
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs108858	0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711599	0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12054220	0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13095034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385306	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406539	0.90[CHD][hapmap]
rs1470142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1654900	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654901	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654924	0.84[ASN][1000 genomes]
rs1682361	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682363	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682364	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682365	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682366	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171519	0.90[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs181732	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183120	0.87[ASN][1000 genomes]
rs183121	0.82[ASN][1000 genomes]
rs2086880	0.85[EUR][1000 genomes]
rs2117008	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2344092	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34564994	0.85[EUR][1000 genomes]
rs361227	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361228	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361229	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361231	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs361232	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361233	0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361234	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361235	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361238	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs361240	0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs361249	0.87[ASN][1000 genomes]
rs361253	0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678275	0.90[CHD][hapmap]
rs4678278	0.86[EUR][1000 genomes]
rs4678281	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678447	0.90[CHD][hapmap]
rs55781515	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439677	0.87[EUR][1000 genomes]
rs6439678	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6766766	0.88[EUR][1000 genomes]
rs6766858	0.88[EUR][1000 genomes]
rs6802479	0.87[EUR][1000 genomes]
rs71620537	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754694	0.86[EUR][1000 genomes]
rs7631541	0.90[CHD][hapmap]
rs7640951	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7646307	0.87[EUR][1000 genomes]
rs7648198	0.90[CHD][hapmap]
rs835627	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835628	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835629	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835630	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835631	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835636	0.90[CHD][hapmap]
rs835637	0.90[CHD][hapmap]
rs835651	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs835652	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900947	0.89[EUR][1000 genomes]
rs900948	0.88[EUR][1000 genomes]
rs900949	0.88[EUR][1000 genomes]
rs900950	0.88[EUR][1000 genomes]
rs9681468	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682783	0.90[CHD][hapmap]
rs9817061	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827066	0.86[EUR][1000 genomes]
rs9845076	0.92[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845460	0.90[CHD][hapmap]
rs9850024	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854795	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9874615	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875855	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999038	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13095028	PCCB	cis	cerebellum	SCAN
rs13095028	PCCB	cis	parietal	SCAN
rs13095028	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136703800-136732400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:136704000-136730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136704800-136731000	Weak transcription	HSMMtube	muscle
4	chr3:136710000-136731000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:136713600-136732800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:136714000-136730800	Weak transcription	HSMM	muscle
7	chr3:136714400-136730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:136715200-136731000	Weak transcription	Adipose Nuclei	Adipose
9	chr3:136715200-136733000	Weak transcription	Left Ventricle	heart
10	chr3:136715400-136730800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:136715600-136730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:136715800-136730400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:136720400-136732400	Weak transcription	Hela-S3	cervix
14	chr3:136720600-136731000	Weak transcription	HMEC	breast
15	chr3:136723800-136732400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:136724600-136730800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:136726000-136730400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:136726000-136732800	Enhancers	Fetal Thymus	thymus
19	chr3:136726600-136732600	Weak transcription	Placenta	Placenta
20	chr3:136726800-136730600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:136727000-136733000	Weak transcription	Fetal Stomach	stomach
22	chr3:136727400-136732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:136727600-136731600	Enhancers	Thymus	Thymus
24	chr3:136727800-136730200	Strong transcription	NHEK	skin
25	chr3:136727800-136730800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:136728000-136733000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:136728000-136733000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:136728200-136732400	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:136728400-136732400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:136728800-136732600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:136729000-136732600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:136729200-136732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:136729600-136732800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:136729800-136730200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:136729800-136730600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:136729800-136731000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:136729800-136733000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:136730000-136733000	Weak transcription	Esophagus	oesophagus

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