Variant report

Variant	rs6311
Chromosome Location	chr13:47471478-47471479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:47471018..47473435-chr16:2203930..2206655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260260	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000131653	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1928040	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs2149434	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4941570	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4941573	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941574	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4942584	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6313	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6561336	0.96[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs731245	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs732821	0.85[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs9316236	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526246	0.96[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9534504	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9534511	0.80[CHD][hapmap]
rs9534513	0.88[CEU][hapmap]
rs9534515	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763019	chr13:47348229-48123447	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6311	GTF2F2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:47466200-47472000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:47467400-47471600	Active TSS	Brain Hippocampus Middle	brain
3	chr13:47467400-47471600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr13:47467600-47471600	Active TSS	NHDF-Ad	bronchial
5	chr13:47467800-47471600	Active TSS	Aorta	Aorta
6	chr13:47468000-47471600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr13:47469000-47471600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:47469000-47472000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:47469200-47471600	Active TSS	Brain Germinal Matrix	brain
10	chr13:47469200-47471600	Active TSS	Fetal Lung	lung
11	chr13:47469600-47471600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:47469800-47472400	Active TSS	Brain Angular Gyrus	brain
13	chr13:47470000-47471600	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr13:47470400-47471600	Active TSS	Fetal Kidney	kidney
15	chr13:47470600-47471600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:47470600-47471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:47471200-47471600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:47471200-47471600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr13:47471200-47471600	Enhancers	Liver	Liver
20	chr13:47471200-47471600	Flanking Active TSS	Fetal Brain Female	brain
21	chr13:47471200-47471600	Enhancers	Fetal Muscle Leg	muscle
22	chr13:47471200-47471600	Bivalent/Poised TSS	Osteobl	bone
23	chr13:47471200-47471800	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:47471200-47472200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:47471200-47472600	Enhancers	Fetal Brain Male	brain
26	chr13:47471200-47473200	Weak transcription	Pancreas	Pancrea
27	chr13:47471400-47471600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:47471400-47471600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:47471400-47471600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr13:47471400-47471600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:47471400-47471600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:47471400-47471600	Active TSS	Adipose Nuclei	Adipose
33	chr13:47471400-47471600	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr13:47471400-47471600	Enhancers	Fetal Stomach	stomach
35	chr13:47471400-47471600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr13:47471400-47471600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr13:47471400-47471800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:47471400-47471800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr13:47471400-47471800	Enhancers	Colon Smooth Muscle	Colon
40	chr13:47471400-47471800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr13:47471400-47472200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr13:47471400-47472400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr13:47471400-47474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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