Variant report

Variant	rs2705124
Chromosome Location	chr12:48880723-48880724
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	MYC	chr12:48880674-48880874	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr12:48880432-48880821	GM12878	blood:	n/a	n/a
3	STAT3	chr12:48880666-48880843	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:48880602-48880927	MCF10A-Er-Src	breast:	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
RPS10P20	TF binding region
C12orf54	TF binding region
ENSG00000177627	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747550	0.93[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs10783262	0.92[CEU][hapmap]
rs1895999	0.93[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2252234	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468351	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2468939	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705131	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2705134	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705156	0.85[AFR][1000 genomes]
rs2731063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731074	0.81[YRI][hapmap]
rs2731092	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2731096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731099	0.89[CHB][hapmap]
rs2731105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731106	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2731111	0.86[AFR][1000 genomes]
rs2732447	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2956465	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956466	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34478996	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34801828	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369449	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4492859	0.85[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs4635128	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139348	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap]
rs71464905	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956260	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2705124	C12orf54	cis	multi-tissue	Pritchard
rs2705124	MGC35033	cis	multi-tissue	Pritchard
rs2705124	C12orf54	cis	lymphoblastoid	seeQTL
rs2705124	ASB8	cis	parietal	SCAN
rs2705124	C12orf54	cis	Esophagus Mucosa	GTEx
rs2705124	GPD1	cis	cerebellum	SCAN
rs2705124	FAM186B	cis	parietal	SCAN

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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