Variant report

Variant	rs12049007
Chromosome Location	chr1:93448516-93448517
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1011663	1.00[ASN][1000 genomes]
rs10747454	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164850	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164851	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120036	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130044	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133990	0.85[ASN][1000 genomes]
rs12144226	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678784	0.93[ASN][1000 genomes]
rs2086314	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127400	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561471	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3943283	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515797	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847226	0.99[ASN][1000 genomes]
rs4847389	0.84[ASN][1000 genomes]
rs514235	0.81[ASN][1000 genomes]
rs521428	0.90[ASN][1000 genomes]
rs534409	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs567613	0.93[ASN][1000 genomes]
rs594527	0.93[ASN][1000 genomes]
rs606344	0.93[ASN][1000 genomes]
rs619784	0.93[ASN][1000 genomes]
rs641462	0.90[ASN][1000 genomes]
rs660870	0.93[ASN][1000 genomes]
rs663112	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671268	0.81[ASN][1000 genomes]
rs6681429	0.81[ASN][1000 genomes]
rs7517539	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7524934	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753391	0.92[ASN][1000 genomes]
rs770883	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs945630	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12049007	FAM69A	Cis_1M	lymphoblastoid	RTeQTL
rs12049007	FAM69A	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93444200-93448800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr1:93445400-93448800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:93447200-93448800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:93448000-93448800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:93448000-93454800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:93448000-93454800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:93448400-93453800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links