Variant report

Variant	rs12548940
Chromosome Location	chr8:51157913-51157914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10092399	0.88[CEU][hapmap]
rs10093604	0.83[CEU][hapmap]
rs10094935	0.88[CEU][hapmap]
rs10109835	0.82[CEU][hapmap]
rs10113812	0.88[CEU][hapmap]
rs10504100	0.87[CHD][hapmap];0.82[YRI][hapmap]
rs10957764	1.00[CHB][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs10957802	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156091	1.00[YRI][hapmap]
rs12540980	1.00[YRI][hapmap]
rs12541707	1.00[JPT][hapmap]
rs12544425	1.00[YRI][hapmap]
rs12544631	0.88[CEU][hapmap]
rs12548399	1.00[YRI][hapmap]
rs13251587	0.88[CEU][hapmap]
rs13251700	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13257386	1.00[YRI][hapmap]
rs13260506	1.00[YRI][hapmap]
rs13261341	1.00[YRI][hapmap]
rs13270234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13280089	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349317	0.88[CEU][hapmap]
rs1450131	1.00[YRI][hapmap]
rs1466128	1.00[YRI][hapmap]
rs1470680	0.82[YRI][hapmap]
rs1548073	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1597426	0.88[CEU][hapmap]
rs17686196	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs17769846	0.82[YRI][hapmap]
rs2044777	1.00[YRI][hapmap]
rs2044778	1.00[YRI][hapmap]
rs2106156	1.00[CHB][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs2157736	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs34160877	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34431441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908792	0.90[ASN][1000 genomes]
rs35418717	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922033	0.83[CEU][hapmap];0.92[GIH][hapmap]
rs4263785	1.00[YRI][hapmap]
rs4379460	1.00[YRI][hapmap]
rs4873141	0.88[CEU][hapmap]
rs4873438	0.88[CEU][hapmap]
rs4873439	0.88[CEU][hapmap]
rs4873442	0.88[CEU][hapmap]
rs4873443	0.88[CEU][hapmap]
rs56413317	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62516686	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999627	0.88[CEU][hapmap]
rs7017642	0.88[CEU][hapmap]
rs7821189	0.88[CEU][hapmap]
rs896023	0.82[YRI][hapmap]
rs9298295	0.88[CEU][hapmap];0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs930671	0.82[YRI][hapmap]

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	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12548940	RNGTT	trans	lymphoblastoid	seeQTL
rs12548940	SNTG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51156800-51161400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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