Variant report

Variant	rs11132959
Chromosome Location	chr4:173646842-173646843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10001933	0.92[CEU][hapmap]
rs10016145	0.87[JPT][hapmap]
rs10024969	0.88[CHB][hapmap]
rs10520242	0.88[CHB][hapmap];0.90[MEX][hapmap]
rs10866355	0.87[ASN][1000 genomes]
rs10866356	0.88[JPT][hapmap]
rs10866357	0.88[JPT][hapmap]
rs10866361	0.81[JPT][hapmap]
rs10866362	0.82[JPT][hapmap]
rs1106651	0.88[ASN][1000 genomes]
rs11132954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11132955	0.81[CHD][hapmap]
rs11132969	0.88[JPT][hapmap]
rs1158684	0.89[CHD][hapmap];0.94[JPT][hapmap]
rs11722378	0.92[ASN][1000 genomes]
rs11725400	0.88[JPT][hapmap]
rs11932974	0.86[MEX][hapmap]
rs11938551	0.82[JPT][hapmap]
rs12499966	0.90[EUR][1000 genomes]
rs12501331	0.86[ASN][1000 genomes]
rs12502034	0.90[EUR][1000 genomes]
rs12505471	0.90[EUR][1000 genomes]
rs12509227	0.90[EUR][1000 genomes]
rs12509744	0.89[ASN][1000 genomes]
rs12510770	0.90[EUR][1000 genomes]
rs12510844	0.86[EUR][1000 genomes]
rs12511707	0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs12511715	0.86[EUR][1000 genomes]
rs12513314	0.88[CHB][hapmap]
rs12642442	0.88[JPT][hapmap]
rs12643395	0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs12643816	0.88[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs12645440	0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs12647340	0.95[CHD][hapmap];0.94[JPT][hapmap]
rs12649426	0.95[CHD][hapmap];0.94[JPT][hapmap]
rs12651320	0.88[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes]
rs13107045	0.92[ASN][1000 genomes]
rs13134194	0.82[JPT][hapmap]
rs13146563	0.94[JPT][hapmap]
rs1347698	0.88[CHB][hapmap]
rs1347700	0.95[CHD][hapmap];0.94[JPT][hapmap]
rs1347702	0.82[CHB][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap]
rs1370581	0.92[ASN][1000 genomes]
rs1437828	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437834	0.88[JPT][hapmap]
rs1437837	1.00[JPT][hapmap]
rs1437840	0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs1437842	0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1540466	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1540468	0.88[CHB][hapmap]
rs1540470	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs1540472	0.82[CHB][hapmap];0.90[MEX][hapmap]
rs1548346	0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1548347	0.88[ASN][1000 genomes]
rs17058683	0.88[CHB][hapmap]
rs17058705	0.83[CHB][hapmap]
rs17058736	0.83[CHB][hapmap]
rs17058752	0.82[CHB][hapmap]
rs17058802	0.88[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs17307651	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs17308839	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs17308944	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1898554	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1946797	0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2043781	0.86[EUR][1000 genomes]
rs2043783	0.81[JPT][hapmap]
rs2118439	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2118441	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2118442	0.92[ASN][1000 genomes]
rs34567973	0.92[ASN][1000 genomes]
rs35184155	0.89[ASN][1000 genomes]
rs35280724	0.92[ASN][1000 genomes]
rs35345168	0.92[ASN][1000 genomes]
rs36081927	0.90[EUR][1000 genomes]
rs4470604	1.00[JPT][hapmap]
rs4522845	0.88[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs4546224	0.82[JPT][hapmap]
rs4569731	1.00[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];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4608790	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4695771	0.92[CHD][hapmap];0.94[JPT][hapmap]
rs4695799	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4695932	0.80[CHB][hapmap]
rs4695991	0.86[EUR][1000 genomes]
rs4696006	1.00[JPT][hapmap]
rs4696014	0.88[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs4696015	0.92[ASN][1000 genomes]
rs4696016	0.92[ASN][1000 genomes]
rs4696022	0.82[JPT][hapmap]
rs4696028	0.88[JPT][hapmap]
rs4696029	0.92[CEU][hapmap]
rs4696031	0.84[CEU][hapmap]
rs58774009	0.85[EUR][1000 genomes]
rs62330792	0.86[EUR][1000 genomes]
rs62330815	0.90[EUR][1000 genomes]
rs62330816	0.90[EUR][1000 genomes]
rs62330818	0.87[EUR][1000 genomes]
rs62330819	0.90[EUR][1000 genomes]
rs62330820	0.90[EUR][1000 genomes]
rs6553645	0.91[ASN][1000 genomes]
rs6553658	0.82[JPT][hapmap]
rs6812449	0.90[EUR][1000 genomes]
rs6819441	0.92[ASN][1000 genomes]
rs6821734	0.83[EUR][1000 genomes]
rs6822571	0.81[JPT][hapmap]
rs6822579	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827154	0.88[CHB][hapmap]
rs6838201	0.90[EUR][1000 genomes]
rs6844200	0.87[CHB][hapmap]
rs6855645	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs7438724	0.87[JPT][hapmap]
rs747493	0.83[CHB][hapmap]
rs748347	0.94[JPT][hapmap]
rs7659511	0.92[CHD][hapmap];0.94[JPT][hapmap]
rs7664183	0.90[EUR][1000 genomes]
rs7672787	0.92[ASN][1000 genomes]
rs7676941	0.92[CEU][hapmap]
rs7681059	0.92[CEU][hapmap]
rs7681189	0.88[JPT][hapmap]
rs7685421	0.88[JPT][hapmap]
rs7691448	0.92[ASN][1000 genomes]
rs7694886	0.90[EUR][1000 genomes]
rs837196	0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap]
rs9312527	0.88[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv880685	chr4:173562564-173661711	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv880613	chr4:173569281-173661711	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3327952	chr4:173591786-173805861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11132959	SAP30	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173645200-173649600	Enhancers	Fetal Intestine Small	intestine
2	chr4:173645600-173647000	Enhancers	Fetal Intestine Large	intestine
3	chr4:173646000-173647000	Enhancers	HepG2	liver
4	chr4:173646400-173647800	Active TSS	A549	lung
5	chr4:173646800-173647000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:173646800-173647200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:173646800-173647400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr4:173646800-173648600	Enhancers	Stomach Mucosa	stomach

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