Variant report

Variant	rs2705127
Chromosome Location	chr12:48883012-48883013
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	chr12:48882700-48883303	GM12878	blood:	n/a	n/a
2	FOS	chr12:48882762-48883225	MCF10A-Er-Src	breast:	n/a	n/a
3	BATF	chr12:48882829-48883217	GM12878	blood:	n/a	chr12:48883023-48883034
4	BHLHE40	chr12:48882898-48883195	GM12878	blood:	n/a	n/a
5	STAT3	chr12:48882874-48883143	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr12:48882896-48883206	MCF10A-Er-Src	breast:	n/a	n/a
7	SP1	chr12:48882811-48883134	GM12878	blood:	n/a	n/a
8	MYC	chr12:48882797-48883582	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr12:48882814-48883236	GM12878	blood:	n/a	n/a
10	SP1	chr12:48882789-48883194	GM12878	blood:	n/a	n/a
11	NFIC	chr12:48882423-48883336	GM12878	blood:	n/a	n/a
12	MYC	chr12:48882824-48883500	MCF10A-Er-Src	breast:	n/a	n/a
13	SRF	chr12:48882914-48883195	GM12878	blood:	n/a	chr12:48883067-48883080 chr12:48883069-48883078 chr12:48883068-48883082 chr12:48883068-48883079
14	IRF4	chr12:48882807-48883262	GM12878	blood:	n/a	n/a
15	EBF1	chr12:48882732-48883206	GM12878	blood:	n/a	chr12:48882931-48882942
16	POLR2A	chr12:48882749-48883524	MCF10A-Er-Src	breast:	n/a	n/a
17	SRF	chr12:48882885-48883223	GM12878	blood:	n/a	chr12:48883067-48883080 chr12:48883069-48883078 chr12:48883068-48883082 chr12:48883068-48883079
18	FOS	chr12:48882837-48883421	MCF10A-Er-Src	breast:	n/a	n/a
19	BCLAF1	chr12:48882751-48883247	GM12878	blood:	n/a	n/a
20	TBP	chr12:48882671-48883205	GM12878	blood:	n/a	n/a
21	BATF	chr12:48882861-48883157	GM12878	blood:	n/a	chr12:48883023-48883034
22	BCL11A	chr12:48882852-48883267	GM12878	blood:	n/a	n/a
23	STAT3	chr12:48882800-48883232	MCF10A-Er-Src	breast:	n/a	n/a
24	EBF1	chr12:48882812-48883124	GM12878	blood:	n/a	chr12:48882931-48882942
25	IRF4	chr12:48882820-48883124	GM12878	blood:	n/a	n/a
26	FOXM1	chr12:48882633-48883283	GM12878	blood:	n/a	n/a
27	FOS	chr12:48882823-48883213	MCF10A-Er-Src	breast:	n/a	n/a
28	ZNF143	chr12:48882852-48883158	GM12878	blood:	n/a	n/a
29	STAT3	chr12:48882896-48883192	GM12878	blood:	n/a	n/a
30	EP300	chr12:48882788-48883206	GM12878	blood:	n/a	n/a
31	E2F4	chr12:48882935-48883203	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr12:48882825-48883232	MCF10A-Er-Src	breast:	n/a	n/a
33	SRF	chr12:48882983-48883111	GM12878	blood:	n/a	chr12:48883067-48883080 chr12:48883069-48883078 chr12:48883068-48883082 chr12:48883068-48883079
34	CEBPB	chr12:48882593-48883325	GM12878	blood:	n/a	n/a
35	STAT3	chr12:48882822-48883227	MCF10A-Er-Src	breast:	n/a	n/a
36	RUNX3	chr12:48882835-48883231	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48882871..48884702-chr12:48885100..48887755,2	K562	blood:

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

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11168613	1.00[JPT][hapmap]
rs12580814	1.00[JPT][hapmap]
rs12581223	1.00[JPT][hapmap]
rs12582811	1.00[CHB][hapmap]
rs17234937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705130	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705131	0.84[AFR][1000 genomes]
rs2731092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731096	0.87[AFR][1000 genomes]
rs2731099	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731100	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731103	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731106	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731108	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4426170	1.00[JPT][hapmap]
rs4547144	1.00[JPT][hapmap]
rs7139348	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294585	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2705127	C12orf54	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48881600-48883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48881600-48884000	Enhancers	HMEC	breast
3	chr12:48882400-48884000	Enhancers	GM12878-XiMat	blood
4	chr12:48882600-48883600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:48882800-48883200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:48882800-48883400	Flanking Active TSS	NHEK	skin
7	chr12:48883000-48883200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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