Variant report

Variant	rs3802754
Chromosome Location	chr11:26682434-26682435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10501059	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10501060	0.93[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10501062	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835042	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835047	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11029649	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11600634	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11601992	0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[ASN][1000 genomes]
rs11602453	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11603245	0.90[ASN][1000 genomes]
rs11603582	0.90[ASN][1000 genomes]
rs11604868	0.90[ASN][1000 genomes]
rs11605160	0.91[ASN][1000 genomes]
rs11606202	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs11606235	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11606418	0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs11606579	0.89[ASN][1000 genomes]
rs12278931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12279760	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12292104	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12295638	0.90[JPT][hapmap]
rs12574098	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575470	0.91[ASN][1000 genomes]
rs12577083	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12577224	0.95[JPT][hapmap]
rs12577354	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916005	0.90[ASN][1000 genomes]
rs3802756	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41468744	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs421694	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4382858	0.95[JPT][hapmap]
rs4418758	0.95[JPT][hapmap]
rs4418759	0.95[JPT][hapmap]
rs55870165	0.91[ASN][1000 genomes]
rs56012427	0.93[EUR][1000 genomes]
rs57160661	0.91[ASN][1000 genomes]
rs58302588	0.91[ASN][1000 genomes]
rs58449812	0.91[ASN][1000 genomes]
rs58629434	0.91[ASN][1000 genomes]
rs58631362	0.91[ASN][1000 genomes]
rs58857364	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59747833	0.90[ASN][1000 genomes]
rs60530378	0.91[ASN][1000 genomes]
rs60600602	0.91[ASN][1000 genomes]
rs61580147	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7101361	0.95[JPT][hapmap]
rs7101811	0.95[JPT][hapmap]
rs7102014	0.95[JPT][hapmap]
rs7102068	0.95[JPT][hapmap]
rs7112752	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7114378	0.95[JPT][hapmap]
rs7116077	0.83[ASN][1000 genomes]
rs7117596	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7126479	0.88[ASN][1000 genomes]
rs7128122	0.95[JPT][hapmap];0.82[LWK][hapmap]
rs7128239	0.95[JPT][hapmap];0.82[LWK][hapmap]
rs7128384	0.95[JPT][hapmap]
rs7128823	0.95[JPT][hapmap];0.82[LWK][hapmap]
rs7932456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932573	0.95[JPT][hapmap]
rs7945253	0.83[ASN][1000 genomes]
rs7945560	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044544	chr11:26506962-26967285	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv916187	chr11:26576875-27328603	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3802754	BBOX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:26682400-26682600	Flanking Active TSS	Fetal Heart	heart
2	chr11:26682400-26683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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