Variant report

Variant	rs17767362
Chromosome Location	chr14:71733790-71733791
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	chr14:71731979..71733968-chr14:71736696..71738464,2	MCF-7	breast:
2	chr1:151998303..152000885-chr14:71732498..71734961,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11620632	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11623477	0.83[EUR][1000 genomes]
rs11626886	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11626990	0.84[EUR][1000 genomes]
rs11627918	0.91[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11845249	0.91[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs11849508	0.85[EUR][1000 genomes]
rs12881643	0.83[EUR][1000 genomes]
rs12894478	0.83[EUR][1000 genomes]
rs17178045	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17178206	1.00[CHB][hapmap]
rs17767380	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17767386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17767392	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767398	0.82[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs17767410	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767446	0.83[EUR][1000 genomes]
rs17767499	0.83[EUR][1000 genomes]
rs17767553	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1990241	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108707	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2108708	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2159145	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2877729	1.00[CHB][hapmap]
rs34011442	0.85[EUR][1000 genomes]
rs34524083	0.83[EUR][1000 genomes]
rs34528013	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34528131	0.83[EUR][1000 genomes]
rs34533948	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34649709	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34674149	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34725136	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34746156	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34748537	0.83[EUR][1000 genomes]
rs34767050	0.82[EUR][1000 genomes]
rs34873919	0.84[EUR][1000 genomes]
rs34911660	0.81[AMR][1000 genomes]
rs34957192	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35051046	0.83[EUR][1000 genomes]
rs35054229	0.81[EUR][1000 genomes]
rs35094946	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35122644	0.85[EUR][1000 genomes]
rs35260692	0.83[EUR][1000 genomes]
rs35468256	0.83[EUR][1000 genomes]
rs35621718	0.85[EUR][1000 genomes]
rs35692397	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35796129	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35822724	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35854505	0.83[EUR][1000 genomes]
rs36057816	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36093218	0.81[EUR][1000 genomes]
rs4453405	0.81[AMR][1000 genomes]
rs4899394	0.81[AMR][1000 genomes]
rs4902928	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55851052	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55863348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55896578	0.82[EUR][1000 genomes]
rs56363446	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57204407	0.80[EUR][1000 genomes]
rs58952176	0.80[EUR][1000 genomes]
rs59697713	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61989240	0.82[EUR][1000 genomes]
rs61989244	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61989245	0.84[EUR][1000 genomes]
rs61989246	0.86[EUR][1000 genomes]
rs61989247	0.84[EUR][1000 genomes]
rs61989250	0.85[EUR][1000 genomes]
rs61989252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61989255	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61989256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61989257	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61989259	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61991192	0.85[EUR][1000 genomes]
rs61991193	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61991195	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61991199	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991200	0.81[AMR][1000 genomes]
rs61991201	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991202	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991203	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991204	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991205	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991247	0.83[EUR][1000 genomes]
rs61991248	0.83[EUR][1000 genomes]
rs61991250	0.83[EUR][1000 genomes]
rs68073803	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7140354	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7142180	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7145755	0.83[EUR][1000 genomes]
rs7147434	0.83[EUR][1000 genomes]
rs7147668	0.83[EUR][1000 genomes]
rs7155259	0.94[CEU][hapmap]
rs7156194	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs7156460	0.83[EUR][1000 genomes]
rs7159252	0.80[EUR][1000 genomes]
rs7160460	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7160587	0.80[EUR][1000 genomes]
rs723966	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs725673	1.00[CHB][hapmap]
rs72726701	0.85[EUR][1000 genomes]
rs72726702	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72728403	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72728406	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72728427	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8007068	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[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	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17767362	SIPA1L1	cis	cerebellum	SCAN
rs17767362	PCNX	cis	cerebellum	SCAN
rs17767362	SLC8A3	cis	cerebellum	SCAN
rs17767362	PCNX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71729600-71734000	Weak transcription	Osteobl	bone
2	chr14:71733600-71733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr14:71733600-71733800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr14:71733600-71734000	Enhancers	Hela-S3	cervix
5	chr14:71733600-71734200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr14:71733600-71734200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:71733600-71734400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:71733600-71734600	Enhancers	Muscle Satellite Cultured Cells	--

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