Variant report

Variant	rs12117429
Chromosome Location	chr1:75633642-75633643
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75590358..75592095-chr1:75633170..75635872,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10493561	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493570	1.00[CHB][hapmap]
rs12132601	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133614	1.00[CHB][hapmap]
rs12138223	1.00[CHB][hapmap]
rs12142460	1.00[CHB][hapmap]
rs12732329	1.00[CHB][hapmap]
rs12751207	1.00[CHB][hapmap]
rs1319656	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1405312	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526511	1.00[CHB][hapmap]
rs1526516	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565565	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17640591	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852348	1.00[CHB][hapmap]
rs1852349	1.00[CHB][hapmap]
rs4949821	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275313	0.86[EUR][1000 genomes]
rs595009	0.93[CEU][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607167	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610159	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695423	1.00[CHB][hapmap]
rs677470	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679258	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684117	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs74094382	1.00[ASN][1000 genomes]
rs7524020	1.00[CHB][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	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12117429	RABGGTB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75632200-75634000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:75632200-75634000	Enhancers	Adipose Nuclei	Adipose
3	chr1:75633400-75634000	Enhancers	Fetal Muscle Leg	muscle
4	chr1:75633600-75634000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links