Variant report

Variant	rs11060167
Chromosome Location	chr12:122676013-122676014
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122675699..122678152-chr12:122686921..122688838,2	MCF-7	breast:
2	chr12:122491891..122492950-chr12:122675163..122676073,7	K562	blood:
3	chr12:122675858..122677484-chr12:122679022..122682895,3	K562	blood:
4	chr12:122674046..122677306-chr12:122708798..122710546,3	K562	blood:
5	chr12:122492288..122492924-chr12:122675554..122676136,3	MCF-7	breast:
6	chr12:122615252..122616214-chr12:122675084..122676097,6	K562	blood:
7	chr12:122661637..122664175-chr12:122674648..122677417,2	K562	blood:
8	chr12:122661637..122663499-chr12:122674584..122677417,2	K562	blood:
9	chr12:122186484..122187293-chr12:122675389..122676074,2	MCF-7	breast:
10	chr12:122615211..122616210-chr12:122675123..122676106,13	MCF-7	breast:
11	chr12:122674327..122677306-chr12:122708798..122710323,2	K562	blood:
12	chr12:122674983..122677095-chr12:122689266..122691695,2	K562	blood:
13	chr12:122675984..122678121-chr12:122679124..122682005,2	K562	blood:
14	chr12:122469175..122470175-chr12:122675088..122676086,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184047	Chromatin interaction
ENSG00000176383	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10848035	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11060333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423987	0.86[CEU][hapmap]
rs12578739	0.87[EUR][1000 genomes]
rs12578815	0.95[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12578863	0.88[EUR][1000 genomes]
rs12810587	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs12814923	0.95[CEU][hapmap]
rs12816400	0.85[EUR][1000 genomes]
rs12816499	0.95[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs12820704	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs12822121	0.86[CEU][hapmap]
rs12824385	0.81[EUR][1000 genomes]
rs12824701	0.86[CEU][hapmap]
rs12824925	0.95[CEU][hapmap]
rs12825149	0.95[CEU][hapmap]
rs12825279	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs12826834	0.88[EUR][1000 genomes]
rs12827843	0.88[EUR][1000 genomes]
rs12831210	0.83[EUR][1000 genomes]
rs1512023	0.86[CEU][hapmap]
rs2068223	0.95[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2271408	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2271409	0.95[CEU][hapmap]
rs35030971	0.81[EUR][1000 genomes]
rs3809116	0.95[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4758649	0.95[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4758677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7388	0.95[CEU][hapmap]
rs872451	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11060167	GPR109A	cis	cerebellum	SCAN
rs11060167	IL31	cis	parietal	SCAN
rs11060167	VPS33A	cis	lymphoblastoid	seeQTL
rs11060167	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122668400-122676400	Weak transcription	Brain Anterior Caudate	brain
2	chr12:122668400-122678400	Weak transcription	Fetal Intestine Small	intestine
3	chr12:122668400-122681600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:122670000-122683600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:122674800-122685000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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