Variant report

Variant	rs17226957
Chromosome Location	chr20:14366896-14366897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13036305	1.00[ASW][hapmap]
rs13036742	0.83[AMR][1000 genomes]
rs13036861	0.80[AMR][1000 genomes]
rs13036915	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13037096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13038046	1.00[CEU][hapmap]
rs13038084	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13039188	0.83[AMR][1000 genomes]
rs13039594	0.83[AMR][1000 genomes]
rs13039619	0.83[AMR][1000 genomes]
rs13039855	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13039862	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13040337	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13040558	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13040987	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13041262	0.89[CEU][hapmap]
rs13041600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs13042179	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13042866	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13043921	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs13044911	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13045655	0.83[AMR][1000 genomes]
rs17226971	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17226999	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17812658	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17812676	1.00[CEU][hapmap]
rs1998236	0.90[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2210655	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34021592	0.95[EUR][1000 genomes]
rs34085437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34287609	0.83[AMR][1000 genomes]
rs34522477	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34538736	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34824714	0.83[AMR][1000 genomes]
rs34880844	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34896694	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34955232	0.83[AMR][1000 genomes]
rs34985688	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35171263	0.83[AMR][1000 genomes]
rs35346025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35438476	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35445955	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35505382	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35511588	0.83[AMR][1000 genomes]
rs35554517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35577212	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35610301	0.83[AMR][1000 genomes]
rs35631624	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35649042	0.83[AMR][1000 genomes]
rs35733982	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35747430	0.83[AMR][1000 genomes]
rs35763852	0.83[AMR][1000 genomes]
rs35943017	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35989081	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36062805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36134325	0.83[AMR][1000 genomes]
rs41328645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4630827	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4814301	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62204373	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62204396	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62204398	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62204402	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62204403	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62204406	0.83[AMR][1000 genomes]
rs62204411	0.83[AMR][1000 genomes]
rs62204429	0.83[AMR][1000 genomes]
rs62204435	0.83[AMR][1000 genomes]
rs62204437	0.83[AMR][1000 genomes]
rs62207626	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62207627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62207628	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74179739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74179740	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74179742	0.83[AMR][1000 genomes]
rs915074	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs915075	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs963329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1061705	chr20:14330029-14430604	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1062079	chr20:14334350-14429820	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1063787	chr20:14341199-14408090	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv585440	chr20:14352394-14457834	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1063733	chr20:14357857-14459453	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17226957	PCSK2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14365400-14368400	Weak transcription	HMEC	breast
2	chr20:14365400-14387000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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