Variant report

Variant	rs10962244
Chromosome Location	chr9:15980320-15980321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 208 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:203)

rs_ID	r²[population]
rs10733305	0.80[CHB][hapmap]
rs10738417	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10738418	0.91[ASN][1000 genomes]
rs10738419	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10738420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10738421	0.91[ASN][1000 genomes]
rs10738422	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10738423	0.84[ASN][1000 genomes]
rs10738424	0.84[ASN][1000 genomes]
rs10756704	0.80[CHB][hapmap]
rs10756709	0.80[CHB][hapmap]
rs10756710	0.80[CHB][hapmap]
rs10756711	0.80[CHB][hapmap]
rs10756714	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10756715	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10756720	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs10756722	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10756724	0.89[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10756725	0.93[ASN][1000 genomes]
rs10756726	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10756728	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10756729	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10756730	0.98[ASN][1000 genomes]
rs10756731	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10756733	0.88[ASN][1000 genomes]
rs10756735	0.84[ASN][1000 genomes]
rs10756736	0.84[ASN][1000 genomes]
rs10756739	0.80[ASN][1000 genomes]
rs1080485	0.83[ASN][1000 genomes]
rs10810446	0.80[CHB][hapmap]
rs10810455	0.80[CHB][hapmap]
rs10810461	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap]
rs10810462	0.90[CHB][hapmap]
rs10810479	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs10810483	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10810484	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs10810485	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10810486	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10810487	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10810488	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[ASN][1000 genomes]
rs10810494	0.90[CHD][hapmap];0.85[AFR][1000 genomes]
rs10810497	0.85[AFR][1000 genomes]
rs10810498	0.85[AFR][1000 genomes]
rs10810501	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10810502	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[ASN][1000 genomes]
rs10810503	0.92[ASN][1000 genomes]
rs10810505	0.93[ASN][1000 genomes]
rs10810506	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10810507	0.93[ASN][1000 genomes]
rs10810508	0.93[ASN][1000 genomes]
rs10810509	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[ASN][1000 genomes]
rs10810510	0.95[ASN][1000 genomes]
rs10810514	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10810519	0.84[ASN][1000 genomes]
rs10810520	0.84[ASN][1000 genomes]
rs10810521	0.84[ASN][1000 genomes]
rs10810522	0.84[ASN][1000 genomes]
rs10810523	0.84[ASN][1000 genomes]
rs10810524	0.80[ASN][1000 genomes]
rs10810526	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10962156	0.80[CHB][hapmap]
rs10962157	0.80[CHB][hapmap]
rs10962158	0.80[CHB][hapmap]
rs10962225	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10962227	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10962256	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11788695	0.84[ASN][1000 genomes]
rs12379234	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12379466	0.85[ASN][1000 genomes]
rs1328265	0.89[ASN][1000 genomes]
rs1328269	0.85[ASN][1000 genomes]
rs1328273	0.86[ASN][1000 genomes]
rs1328274	0.86[ASN][1000 genomes]
rs1328276	0.83[ASN][1000 genomes]
rs1328278	0.84[ASN][1000 genomes]
rs1328279	0.84[ASN][1000 genomes]
rs1328280	0.84[ASN][1000 genomes]
rs1328283	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1328286	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs13296360	0.80[CHB][hapmap]
rs13297383	0.82[ASN][1000 genomes]
rs1341732	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1341737	0.80[CHB][hapmap]
rs1341738	0.80[CHB][hapmap]
rs1359950	0.81[ASN][1000 genomes]
rs1359952	0.86[JPT][hapmap]
rs1410444	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1410450	0.80[ASN][1000 genomes]
rs1410451	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1539172	0.80[CHB][hapmap]
rs1539173	0.80[CHB][hapmap]
rs1576171	0.89[ASN][1000 genomes]
rs1590749	0.91[ASN][1000 genomes]
rs1590750	0.92[ASN][1000 genomes]
rs1887664	0.94[ASN][1000 genomes]
rs1887666	0.84[ASN][1000 genomes]
rs1887668	0.84[ASN][1000 genomes]
rs1927696	0.86[JPT][hapmap]
rs1927698	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1927699	0.89[ASN][1000 genomes]
rs1927700	0.89[ASN][1000 genomes]
rs1927701	0.89[ASN][1000 genomes]
rs1927702	0.89[ASN][1000 genomes]
rs2017943	0.84[ASN][1000 genomes]
rs2094522	0.85[ASN][1000 genomes]
rs2185663	0.80[CHB][hapmap]
rs2225181	0.86[JPT][hapmap]
rs2225182	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2382540	0.80[CHB][hapmap]
rs2382543	0.87[ASN][1000 genomes]
rs2382544	0.87[ASN][1000 genomes]
rs2382545	0.84[ASN][1000 genomes]
rs2382546	0.81[ASN][1000 genomes]
rs2382547	0.82[ASN][1000 genomes]
rs2891003	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2987008	0.88[ASN][1000 genomes]
rs2987009	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2987010	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2987011	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2987012	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2987013	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2987014	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2987016	0.89[ASN][1000 genomes]
rs2987017	0.89[ASN][1000 genomes]
rs2987019	0.89[ASN][1000 genomes]
rs2987020	0.89[ASN][1000 genomes]
rs2987021	0.89[ASN][1000 genomes]
rs2987022	0.89[ASN][1000 genomes]
rs2987023	0.88[ASN][1000 genomes]
rs2987024	0.89[ASN][1000 genomes]
rs2987025	0.89[ASN][1000 genomes]
rs2987039	0.84[ASN][1000 genomes]
rs2987041	0.84[ASN][1000 genomes]
rs2987042	0.84[ASN][1000 genomes]
rs2987079	0.83[ASN][1000 genomes]
rs2987081	0.84[ASN][1000 genomes]
rs2987086	0.84[ASN][1000 genomes]
rs2987096	0.83[ASN][1000 genomes]
rs3008666	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3008672	0.84[ASN][1000 genomes]
rs3008681	0.90[JPT][hapmap]
rs3008719	0.84[ASN][1000 genomes]
rs3008723	0.84[ASN][1000 genomes]
rs3008726	0.84[ASN][1000 genomes]
rs3008727	0.84[ASN][1000 genomes]
rs3008728	0.84[ASN][1000 genomes]
rs3008729	0.83[ASN][1000 genomes]
rs3008730	0.84[ASN][1000 genomes]
rs3008732	0.82[ASN][1000 genomes]
rs3008736	0.89[ASN][1000 genomes]
rs3008739	0.89[ASN][1000 genomes]
rs3008742	0.89[ASN][1000 genomes]
rs3008744	0.88[ASN][1000 genomes]
rs3008745	0.89[ASN][1000 genomes]
rs3008747	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3008748	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3008749	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3008753	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3118736	0.89[ASN][1000 genomes]
rs3824502	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4146290	0.80[CHB][hapmap]
rs4146291	1.00[LWK][hapmap]
rs4146293	0.80[CHB][hapmap]
rs4247294	0.84[ASN][1000 genomes]
rs4442245	0.81[ASN][1000 genomes]
rs4472620	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4475627	0.84[ASN][1000 genomes]
rs4582646	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4740628	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4740629	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4740632	0.84[ASN][1000 genomes]
rs4741545	0.80[CHB][hapmap];1.00[LWK][hapmap]
rs4741546	0.80[CHB][hapmap];1.00[LWK][hapmap]
rs4741548	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4741552	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4741553	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4741557	0.84[ASN][1000 genomes]
rs4961433	0.85[AFR][1000 genomes]
rs4961526	0.85[AFR][1000 genomes]
rs6474987	0.88[ASN][1000 genomes]
rs6474988	0.88[ASN][1000 genomes]
rs6474989	0.89[ASN][1000 genomes]
rs7023326	0.89[ASN][1000 genomes]
rs7043770	0.80[CHB][hapmap]
rs723756	0.84[ASN][1000 genomes]
rs735962	0.86[JPT][hapmap]
rs752489	0.84[ASN][1000 genomes]
rs752490	0.84[ASN][1000 genomes]
rs769151	0.90[CHD][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes]
rs7849380	0.80[CHB][hapmap]
rs7860528	0.80[CHB][hapmap]
rs7860755	0.80[CHB][hapmap]
rs7873776	0.80[CHB][hapmap]
rs9406581	0.84[ASN][1000 genomes]
rs9407702	0.89[ASN][1000 genomes]
rs943787	0.84[ASN][1000 genomes]
rs943788	0.84[ASN][1000 genomes]
rs943789	0.84[ASN][1000 genomes]
rs961117	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9969685	0.93[ASN][1000 genomes]
rs9969791	0.85[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs9969816	0.93[ASN][1000 genomes]
rs9969817	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753625	chr9:15914055-15980320	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
3	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10962244	PGBD4	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15952600-15987600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:15973200-15988000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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