Variant report

Variant	rs9829484
Chromosome Location	chr3:19345366-19345367
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10510488	0.81[MEX][hapmap]
rs12637672	0.80[EUR][1000 genomes]
rs13060503	0.92[EUR][1000 genomes]
rs13072922	0.81[MEX][hapmap]
rs13078049	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13081910	0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs13083035	0.92[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs13094042	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs17005833	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs17005887	0.85[CEU][hapmap]
rs17570934	0.81[MEX][hapmap]
rs2053507	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6806328	0.83[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs7635327	0.81[MEX][hapmap]
rs7653013	0.82[EUR][1000 genomes]
rs9819481	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836707	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9845765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517847	chr3:18845347-19483695	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9829484	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19329600-19351400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:19343600-19358200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:19344000-19350000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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