Variant report

Variant	rs12039256
Chromosome Location	chr1:93504045-93504046
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11164860	0.84[ASN][1000 genomes]
rs11164861	0.88[ASN][1000 genomes]
rs12022729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023767	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027025	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043007	0.83[CHB][hapmap]
rs12043577	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119421	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130551	0.88[ASN][1000 genomes]
rs12134501	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141895	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678778	0.96[ASN][1000 genomes]
rs2086312	0.86[ASN][1000 genomes]
rs2253595	0.92[ASN][1000 genomes]
rs2492898	0.99[ASN][1000 genomes]
rs2815417	0.89[JPT][hapmap]
rs2928183	0.87[ASN][1000 genomes]
rs4626900	0.99[ASN][1000 genomes]
rs4847227	0.95[ASN][1000 genomes]
rs485336	1.00[ASN][1000 genomes]
rs486370	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs492054	0.83[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs492754	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs493980	0.83[JPT][hapmap]
rs496465	0.83[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs497540	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs504418	0.96[ASN][1000 genomes]
rs517856	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521527	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs524045	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536837	0.84[ASN][1000 genomes]
rs544051	0.82[ASN][1000 genomes]
rs544285	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs553396	0.84[ASN][1000 genomes]
rs557812	0.94[ASN][1000 genomes]
rs56320266	0.88[ASN][1000 genomes]
rs572131	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs57478994	0.99[ASN][1000 genomes]
rs590296	0.96[ASN][1000 genomes]
rs591820	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs591868	0.84[ASN][1000 genomes]
rs592751	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs638462	0.82[ASN][1000 genomes]
rs638958	0.82[ASN][1000 genomes]
rs664524	0.92[ASN][1000 genomes]
rs664852	0.93[ASN][1000 genomes]
rs6674738	0.84[ASN][1000 genomes]
rs680285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs808833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9787147	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs12039256	FAM69A	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93488000-93504200	Enhancers	Fetal Thymus	thymus
2	chr1:93495800-93504200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:93499400-93505000	Enhancers	Dnd41	blood
4	chr1:93499800-93507800	Weak transcription	K562	blood
5	chr1:93500400-93507800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:93501600-93507600	Weak transcription	Thymus	Thymus
7	chr1:93502400-93506600	Weak transcription	HepG2	liver
8	chr1:93503800-93504200	Enhancers	GM12878-XiMat	blood
9	chr1:93503800-93507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:93504000-93507600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:93504000-93507600	Weak transcription	Rectal Mucosa Donor 31	rectum

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