Variant report

Variant	rs914309
Chromosome Location	chr20:24892715-24892716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1029032	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11087480	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11906401	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11906511	0.86[EUR][1000 genomes]
rs12479636	1.00[ASN][1000 genomes]
rs2064404	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs2150644	0.90[EUR][1000 genomes]
rs4239751	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs4462847	1.00[ASN][1000 genomes]
rs4502500	1.00[ASN][1000 genomes]
rs4815358	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4815359	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs55651048	0.81[EUR][1000 genomes]
rs55681373	0.87[EUR][1000 genomes]
rs56053259	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56148678	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56183883	1.00[ASN][1000 genomes]
rs56249107	0.82[EUR][1000 genomes]
rs56299926	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56406017	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58353086	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6036939	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036940	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6036948	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6050026	0.84[EUR][1000 genomes]
rs6050052	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6050056	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6050066	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6050121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050122	1.00[ASN][1000 genomes]
rs6050123	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6050124	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050125	1.00[ASN][1000 genomes]
rs6050127	1.00[ASN][1000 genomes]
rs6050128	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6050129	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6050199	0.88[CEU][hapmap]
rs6076288	0.80[EUR][1000 genomes]
rs6076289	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6076291	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6076293	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6083638	0.83[EUR][1000 genomes]
rs6083645	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6083646	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6083647	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083649	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6083650	0.81[EUR][1000 genomes]
rs6083651	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6083653	0.82[EUR][1000 genomes]
rs6083657	0.82[EUR][1000 genomes]
rs6083697	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6083714	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6106957	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6106965	0.81[AMR][1000 genomes]
rs6106967	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6106969	1.00[ASN][1000 genomes]
rs6114893	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73108128	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73110258	0.90[EUR][1000 genomes]
rs73110260	0.90[EUR][1000 genomes]
rs761368	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs765834	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs8114708	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8114760	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8119191	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8120506	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8123541	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs885402	1.00[ASN][1000 genomes]
rs914308	0.84[EUR][1000 genomes]
rs914310	1.00[ASN][1000 genomes]
rs914311	1.00[ASN][1000 genomes]
rs914312	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs914313	1.00[ASN][1000 genomes]
rs914315	1.00[ASN][1000 genomes]
rs944503	1.00[ASN][1000 genomes]
rs961218	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv432115	chr20:24871385-24915839	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058559	chr20:24880415-24923818	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060158	chr20:24887819-24918081	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1066090	chr20:24887819-24923818	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065568	chr20:24887819-24925706	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs914309	FOXA2	cis	cerebellum	SCAN
rs914309	C20orf3	cis	parietal	SCAN
rs914309	C20orf191	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24891400-24893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24891800-24896000	Weak transcription	Spleen	Spleen
3	chr20:24892000-24892800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr20:24892600-24898600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links