Variant report

Variant	rs17132215
Chromosome Location	chr7:48324897-48324898
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10248040	0.87[JPT][hapmap]
rs10250034	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10279899	0.84[EUR][1000 genomes]
rs10499678	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983863	0.90[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs12666513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12671292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358066	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1526095	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1526099	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1526105	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs17712293	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs17712567	0.85[CHB][hapmap]
rs1997123	0.87[JPT][hapmap]
rs34967126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917172	0.86[EUR][1000 genomes]
rs59328053	0.95[ASN][1000 genomes]
rs6583541	0.84[EUR][1000 genomes]
rs6943279	0.87[JPT][hapmap]
rs6943725	0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6945480	0.84[CHB][hapmap]
rs6949474	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6955212	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6970910	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974746	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7776605	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7778355	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7795198	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7797192	0.87[EUR][1000 genomes]
rs7797332	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7802049	0.87[JPT][hapmap]
rs9692496	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1033738	chr7:48143988-48349357	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv817336	chr7:48238233-48563988	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1022980	chr7:48243227-48567060	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv538833	chr7:48243227-48567060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1022578	chr7:48244414-48584664	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1023575	chr7:48244414-48586685	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1015183	chr7:48244414-48588598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1032135	chr7:48293104-48414154	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1032221	chr7:48302789-48546684	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv533811	chr7:48313757-48482470	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1015399	chr7:48321542-48544359	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17132215	ABCA13	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48319800-48382200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:48320400-48325000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:48320600-48338000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:48322000-48325000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:48322000-48325000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:48322600-48333800	Weak transcription	Spleen	Spleen
7	chr7:48324600-48325200	Enhancers	NHLF	lung
8	chr7:48324800-48325200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:48324800-48325200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:48324800-48325400	Enhancers	HMEC	breast
11	chr7:48324800-48326600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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