Variant report

Variant	rs1470142
Chromosome Location	chr3:136755982-136755983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs108858	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711599	0.89[CHD][hapmap]
rs12054220	0.89[CHD][hapmap]
rs13095028	0.81[CHD][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs13095034	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1385306	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654900	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1654901	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682361	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682363	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682364	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682365	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682366	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16844241	0.82[CHB][hapmap]
rs171519	0.89[CHD][hapmap]
rs181732	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2086880	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2117008	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2344092	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34564994	0.81[EUR][1000 genomes]
rs361227	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361228	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361229	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs361233	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361234	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs361235	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361240	0.89[CHD][hapmap]
rs361253	0.89[CHD][hapmap]
rs4678275	0.89[CHD][hapmap]
rs4678278	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4678281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781515	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439677	0.83[EUR][1000 genomes]
rs6439678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763000	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6763556	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6766766	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6766858	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6802479	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71620537	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754694	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7640951	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7646307	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7648198	0.89[CHD][hapmap]
rs835627	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835628	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835629	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835630	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835631	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835636	0.89[CHD][hapmap]
rs835637	0.89[CHD][hapmap]
rs835651	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs900947	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs900948	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs900949	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs900950	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9681468	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9817061	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827066	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9845076	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9845460	0.89[CHD][hapmap]
rs9850024	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854795	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9874615	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875855	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs999038	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv4028	chr3:136752048-136777353	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1470142	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136752000-136756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:136752000-136764600	Weak transcription	Esophagus	oesophagus
3	chr3:136754600-136760200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:136754800-136757000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:136755000-136757600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:136755000-136765200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:136755400-136756000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:136755600-136758800	Strong transcription	NHEK	skin

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