Variant report

Variant	rs11733055
Chromosome Location	chr4:122275299-122275300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11942481	0.84[AMR][1000 genomes]
rs11945502	0.84[AMR][1000 genomes]
rs1398905	0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17051340	0.84[AMR][1000 genomes]
rs17437266	0.85[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs2013534	0.92[JPT][hapmap]
rs2276955	0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2276956	0.81[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2276958	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2302309	0.85[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3822228	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs41375944	0.85[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4273489	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273490	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4312778	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4642270	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55714487	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs55766300	0.84[AMR][1000 genomes]
rs55928909	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56208410	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351803	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60657864	0.82[AMR][1000 genomes]
rs60938835	0.84[AMR][1000 genomes]
rs61062284	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62319023	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62319028	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319044	0.80[AFR][1000 genomes]
rs62319045	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6813974	0.92[JPT][hapmap]
rs6839915	0.92[JPT][hapmap]
rs72668963	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698313	0.94[GIH][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes]
rs871646	0.84[AMR][1000 genomes]
rs882865	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv4494	chr4:122256838-122290461	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1009199	chr4:122273631-122284157	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv1014399	chr4:122273631-122285135	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
9	nsv1003747	chr4:122273631-122291131	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
10	nsv1014710	chr4:122273631-122292143	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1002113	chr4:122274144-122284157	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	nsv1005642	chr4:122274144-122285135	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	nsv1001804	chr4:122274642-122285135	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11733055	SNORA24	cis	parietal	SCAN
rs11733055	TMEM155	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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