Variant report

Variant	rs4492859
Chromosome Location	chr12:48935308-48935309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48934748..48937258-chr12:49020074..49022107,2	K562	blood:
2	chr12:48934471..48935404-chr12:49011968..49012486,2	K562	blood:
3	chr12:48933826..48935713-chr12:49066983..49069233,2	MCF-7	breast:
4	chr12:48934973..48936541-chr12:49010116..49012626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224709	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10747550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168624	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1895999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs2468351	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2705124	0.85[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs2705125	0.93[CEU][hapmap]
rs2705134	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2705143	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705156	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731063	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs2731078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731079	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731092	0.83[GIH][hapmap]
rs2731096	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs2731105	0.85[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap]
rs2956465	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7139348	0.83[GIH][hapmap]
rs7309958	0.93[CEU][hapmap]
rs7974371	0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1047600	chr12:48927514-48954225	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1048307	chr12:48927514-48958949	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4492859	C12orf54	cis	lymphoblastoid	seeQTL
rs4492859	FAM186B	cis	parietal	SCAN
rs4492859	FMNL3	cis	parietal	SCAN
rs4492859	C12orf54	cis	multi-tissue	Pritchard
rs4492859	RACGAP1	cis	cerebellum	SCAN
rs4492859	C12orf54	cis	Esophagus Mucosa	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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