Variant report

Variant	rs361233
Chromosome Location	chr3:136728357-136728358
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136467223..136474337-chr3:136727110..136735930,17	K562	blood:
2	chr3:136469703..136474003-chr3:136727974..136735265,9	MCF-7	breast:
3	chr3:136469274..136471214-chr3:136728329..136730848,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs108858	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711599	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs12054220	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs12629000	0.86[CHB][hapmap]
rs13095028	0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs13095034	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385306	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406539	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs1470142	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1654900	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654901	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654924	0.84[ASN][1000 genomes]
rs1682361	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682362	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682363	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682364	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682365	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682366	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16844241	1.00[CHB][hapmap]
rs171519	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs181732	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183120	0.87[ASN][1000 genomes]
rs183121	0.82[ASN][1000 genomes]
rs2086880	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2117008	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2344092	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34564994	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361227	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361228	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361229	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361231	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs361232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361234	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361238	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs361240	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs361249	0.87[ASN][1000 genomes]
rs361253	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4678275	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs4678278	0.86[EUR][1000 genomes]
rs4678281	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678447	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs55781515	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439677	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439678	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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754694	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7610507	0.86[CHB][hapmap]
rs7631541	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs7640951	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7646307	0.87[EUR][1000 genomes]
rs7648198	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs835627	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835628	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835630	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835631	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835636	1.00[CHD][hapmap]
rs835637	1.00[CHD][hapmap]
rs835651	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs835652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682783	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs9817061	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827066	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9845076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845460	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs9850024	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854795	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9874615	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875855	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999038	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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
rs361233	PCCB	cis	parietal	SCAN
rs361233	PCCB	cis	cerebellum	SCAN
rs361233	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:32 , 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	chr3:136715000-136729000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:136715200-136731000	Weak transcription	Adipose Nuclei	Adipose
10	chr3:136715200-136733000	Weak transcription	Left Ventricle	heart
11	chr3:136715400-136730800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:136715600-136730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:136715800-136730400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:136720400-136729000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:136720400-136729000	Weak transcription	Esophagus	oesophagus
16	chr3:136720400-136732400	Weak transcription	Hela-S3	cervix
17	chr3:136720600-136731000	Weak transcription	HMEC	breast
18	chr3:136723800-136732400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:136724600-136730800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:136725200-136729800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:136726000-136730400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:136726000-136732800	Enhancers	Fetal Thymus	thymus
23	chr3:136726600-136732600	Weak transcription	Placenta	Placenta
24	chr3:136726800-136730600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:136727000-136733000	Weak transcription	Fetal Stomach	stomach
26	chr3:136727400-136732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:136727600-136731600	Enhancers	Thymus	Thymus
28	chr3:136727800-136730200	Strong transcription	NHEK	skin
29	chr3:136727800-136730800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:136728000-136733000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:136728000-136733000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:136728200-136732400	Weak transcription	Brain Hippocampus Middle	brain

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