Variant report

Variant	rs477855
Chromosome Location	chr11:120094570-120094571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120088424..120091961-chr11:120094010..120097522,6	K562	blood:
2	chr11:120082525..120086305-chr11:120094464..120096217,3	K562	blood:
3	chr11:120081505..120083755-chr11:120092635..120094681,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1287394	0.93[ASN][1000 genomes]
rs2465653	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465654	0.92[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2953362	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499434	0.80[ASN][1000 genomes]
rs531698	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs537089	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs541857	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576263	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs477855	POU2F3	cis	Stomach	GTEx
rs477855	POU2F3	cis	Heart Left Ventricle	GTEx
rs477855	POU2F3	cis	Esophagus Muscularis	GTEx
rs477855	POU2F3	cis	Adipose Subcutaneous	GTEx
rs477855	POU2F3	cis	Nerve Tibial	GTEx
rs477855	CPD	trans	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120082800-120095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:120084200-120102600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:120084600-120095400	Weak transcription	Fetal Kidney	kidney
4	chr11:120086400-120097000	Weak transcription	NHEK	skin
5	chr11:120086600-120095800	Weak transcription	NH-A	brain
6	chr11:120089800-120095600	Weak transcription	Lung	lung
7	chr11:120089800-120099600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:120090200-120095800	Weak transcription	Fetal Heart	heart
9	chr11:120090400-120095400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:120090800-120095400	Weak transcription	Fetal Lung	lung
11	chr11:120090800-120095600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:120090800-120099600	Weak transcription	NHDF-Ad	bronchial
13	chr11:120091000-120094600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:120091000-120095600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:120091000-120096600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:120091000-120097400	Weak transcription	NHLF	lung
17	chr11:120091000-120097600	Genic enhancers	Liver	Liver
18	chr11:120091000-120102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:120091200-120095400	Weak transcription	HSMM	muscle
20	chr11:120091200-120096800	Enhancers	Adipose Nuclei	Adipose
21	chr11:120091200-120097000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:120091400-120095000	Strong transcription	Fetal Stomach	stomach
23	chr11:120091400-120095400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:120091600-120095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:120091800-120095200	Weak transcription	Placenta	Placenta
26	chr11:120091800-120097600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:120092000-120094600	Weak transcription	Left Ventricle	heart
28	chr11:120092000-120094600	Enhancers	Spleen	Spleen
29	chr11:120092000-120095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:120092200-120095600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr11:120092200-120095600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:120092400-120094600	Weak transcription	Ovary	ovary
33	chr11:120092600-120095600	Weak transcription	GM12878-XiMat	blood
34	chr11:120092600-120096400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:120092800-120094600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:120092800-120095000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:120092800-120095400	Weak transcription	Fetal Thymus	thymus
38	chr11:120092800-120095600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:120092800-120095600	Weak transcription	Brain Substantia Nigra	brain
40	chr11:120092800-120095800	Weak transcription	Brain Anterior Caudate	brain
41	chr11:120092800-120097000	Weak transcription	Gastric	stomach
42	chr11:120092800-120102000	Weak transcription	Brain Angular Gyrus	brain
43	chr11:120093000-120095400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:120093000-120095400	Weak transcription	Colonic Mucosa	Colon
45	chr11:120093000-120095400	Strong transcription	Fetal Intestine Large	intestine
46	chr11:120093000-120095600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:120093000-120096400	Weak transcription	Esophagus	oesophagus
48	chr11:120093200-120094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:120093600-120094600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:120093600-120095200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links