Variant report

Variant	rs4078166
Chromosome Location	chr3:133435979-133435980
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133431282..133433899-chr3:133433909..133436143,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10935085	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1130459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464937	0.86[JPT][hapmap]
rs1534166	0.92[JPT][hapmap]
rs35553929	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3811657	0.93[JPT][hapmap]
rs4241357	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4287912	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4443173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4854596	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4994581	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439434	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439436	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782434	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804904	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8177179	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177191	0.93[JPT][hapmap]
rs8177213	0.86[JPT][hapmap]
rs9824479	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830001	0.86[JPT][hapmap]
rs9843635	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9869311	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872999	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
3	nsv963279	chr3:133426521-133449029	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4078166	TF	cis	Skin Sun Exposed Lower leg	GTEx
rs4078166	TFP1	cis	Esophagus Mucosa	GTEx
rs4078166	TF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133412200-133437600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:133418800-133437600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:133431200-133436000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:133431600-133436200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:133433200-133439400	Weak transcription	Ovary	ovary
6	chr3:133433800-133438000	Enhancers	HepG2	liver
7	chr3:133434200-133437000	Enhancers	Brain Substantia Nigra	brain
8	chr3:133434800-133437000	Enhancers	Brain Angular Gyrus	brain
9	chr3:133434800-133437000	Enhancers	Brain Hippocampus Middle	brain
10	chr3:133435400-133436800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:133435600-133436400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:133435800-133436600	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links