Variant report

Variant	rs2731092
Chromosome Location	chr12:48880550-48880551
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	PBX3	chr12:48880503-48880666	GM12878	blood:	n/a	n/a
2	RUNX3	chr12:48880432-48880821	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48880029..48882865-chr12:48884102..48887272,3	K562	blood:
2	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:

Variant related genes	Relation type
C12orf54	TF binding region
RPS10P20	TF binding region
ENSG00000177627	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1807757	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs2705124	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2705125	0.89[CHB][hapmap]
rs2705127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705130	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705131	0.82[AFR][1000 genomes]
rs2705133	0.82[YRI][hapmap]
rs2731063	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2731066	0.81[YRI][hapmap]
rs2731091	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2731094	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2731096	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs2731099	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]
rs2731100	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731102	0.84[CEU][hapmap]
rs2731103	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731105	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap]
rs2731106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731108	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956467	0.84[CEU][hapmap]
rs4369449	0.80[CHB][hapmap]
rs4492859	0.83[GIH][hapmap]
rs7139348	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294585	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309958	0.90[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	nsv975415	chr12:48873981-48881500	Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2731092	C12orf54	cis	lymphoblastoid	seeQTL
rs2731092	C12orf54	cis	Esophagus Mucosa	GTEx
rs2731092	RPAP3	cis	cerebellum	SCAN
rs2731092	C12orf54	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48879800-48881200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48880000-48881200	Enhancers	HMEC	breast
3	chr12:48880400-48880800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:48880400-48880800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:48880400-48880800	Enhancers	GM12878-XiMat	blood
6	chr12:48880400-48881000	Flanking Active TSS	NHEK	skin

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