Variant report

Variant	rs2731078
Chromosome Location	chr12:48926042-48926043
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747550	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783262	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168624	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2468351	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2705134	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2705143	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705156	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731079	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956465	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4492859	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974371	0.87[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	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2731078	C12orf54	cis	multi-tissue	Pritchard
rs2731078	C12orf54	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48924400-48927800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48924600-48926200	Enhancers	Primary T cells from cord blood	blood
3	chr12:48924600-48927800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr12:48925200-48927800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:48925200-48928000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr12:48925400-48926600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:48925400-48927400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:48926000-48927400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:48926000-48927600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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

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