Variant report

Variant	rs3812147
Chromosome Location	chr6:82554804-82554805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM46A-2	chr6:82553501-82555626	XLOC_005774
2	lnc-FAM46A-2	chr6:82554490-82555626	NONHSAT113750

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10455392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10455395	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455396	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10484870	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12189633	0.83[ASN][1000 genomes]
rs12190482	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12192690	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12194273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12196654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12201948	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12203649	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12210686	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12214571	0.83[EUR][1000 genomes]
rs12216177	0.83[ASN][1000 genomes]
rs12662590	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1291466	0.82[ASN][1000 genomes]
rs1931621	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194603	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs194629	0.81[CEU][hapmap]
rs194630	0.81[CEU][hapmap]
rs194634	0.81[CEU][hapmap]
rs194635	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs194636	0.84[MEX][hapmap]
rs3763244	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56710219	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6940643	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs733415	0.82[ASN][1000 genomes]
rs915123	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs926856	0.81[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830712	chr6:82491029-82654531	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3812147	FAM46A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82549800-82556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:82552200-82555600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:82553200-82555800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:82553400-82559000	Weak transcription	Left Ventricle	heart
5	chr6:82553600-82556800	Weak transcription	HepG2	liver
6	chr6:82553600-82557000	Weak transcription	Stomach Mucosa	stomach
7	chr6:82553800-82556200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:82554400-82555200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:82554400-82556200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:82554600-82555000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:82554600-82555200	Enhancers	Osteobl	bone
12	chr6:82554600-82555400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:82554600-82556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:82554800-82555600	Enhancers	Aorta	Aorta
15	chr6:82554800-82556000	Enhancers	Ovary	ovary

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