Variant report

Variant	rs2705134
Chromosome Location	chr12:48889908-48889909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48887453..48890090-chr12:48892571..48894412,2	MCF-7	breast:
2	chr12:48888880..48891853-chr12:48895392..48897603,2	MCF-7	breast:
3	chr12:48887538..48890353-chr12:48917589..48920002,2	K562	blood:

Variant related genes	Relation type
ENSG00000197376	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10747550	0.84[AMR][1000 genomes]
rs10783262	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2252234	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2468351	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2468939	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2705124	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705125	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705131	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705143	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2705156	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2731063	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731078	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2731079	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2731096	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731105	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731111	0.96[AFR][1000 genomes]
rs2732447	0.82[ASN][1000 genomes]
rs2956465	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956466	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34478996	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34801828	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4492859	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4635128	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71464905	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309958	0.82[ASN][1000 genomes]
rs7956260	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv975416	chr12:48882416-48893049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2705134	C12orf54	cis	multi-tissue	Pritchard
rs2705134	C12orf54	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48887000-48891800	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:48887600-48890000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:48888800-48891000	Weak transcription	Spleen	Spleen

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