Variant report

Variant	rs2731099
Chromosome Location	chr12:48883926-48883927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr12:48883878-48884459	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48875260..48877080-chr12:48883909..48886028,2	K562	blood:
2	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:
3	chr12:48882871..48884702-chr12:48885100..48887755,2	K562	blood:

Variant related genes	Relation type
C12orf54	TF binding region
ENSG00000240443	Chromatin interaction
ENSG00000177627	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1807757	0.91[CEU][hapmap]
rs2705124	0.89[CHB][hapmap]
rs2705125	0.81[CHB][hapmap]
rs2705127	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705130	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705131	0.85[AFR][1000 genomes]
rs2705133	0.81[YRI][hapmap]
rs2731063	0.89[CHB][hapmap]
rs2731091	0.84[CEU][hapmap]
rs2731092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731094	0.84[CEU][hapmap]
rs2731096	0.89[CHB][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs2731100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731102	0.84[CEU][hapmap]
rs2731103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731105	0.89[CHB][hapmap]
rs2731106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956467	0.85[CEU][hapmap]
rs7139348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294585	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309958	0.81[CHB][hapmap];0.81[YRI][hapmap]

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
rs2731099	C12orf54	cis	Esophagus Mucosa	GTEx
rs2731099	C12orf54	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48881600-48884000	Enhancers	HMEC	breast
2	chr12:48882400-48884000	Enhancers	GM12878-XiMat	blood
3	chr12:48883200-48884000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:48883400-48884000	Enhancers	NHEK	skin
5	chr12:48883800-48885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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