Variant report

Variant	rs6439439
Chromosome Location	chr3:133481498-133481499
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:133470213-133490385	HepG2	liver:	n/a	n/a
2	MBD4	chr3:133480265-133482101	HepG2	liver:	n/a	n/a
3	HEY1	chr3:133470261-133482084	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:133479434-133482047	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:133471516-133487597	HepG2	liver:	n/a	n/a
6	MBD4	chr3:133479369-133483413	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133480882-133484500	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:133479294-133484913	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:133470633-133487808	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133380292..133382359-chr3:133479467..133482336,2	K562	blood:
2	chr3:133475218..133478981-chr3:133481312..133484055,3	K562	blood:

Variant related genes	Relation type
TF	TF binding region
ENSG00000163781	Chromatin interaction
ENSG00000242337	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12595	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358024	0.81[ASN][1000 genomes]
rs1525889	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34252038	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34805309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811647	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811658	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854760	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854761	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854762	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6762719	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794945	0.80[EUR][1000 genomes]
rs6797713	0.83[AMR][1000 genomes]
rs7638018	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8177240	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177245	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177247	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177248	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177252	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177253	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177256	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177259	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177260	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177261	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177262	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177271	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177272	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177295	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9813689	0.80[EUR][1000 genomes]
rs9843728	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871148	0.80[EUR][1000 genomes]
rs9882812	0.80[EUR][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	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	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv877508	chr3:133476852-133482662	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133465600-133483000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:133475000-133487000	Weak transcription	Fetal Brain Male	brain
3	chr3:133475200-133482800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:133477000-133490400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:133478800-133482600	Weak transcription	Left Ventricle	heart
6	chr3:133479600-133482400	Strong transcription	Brain Cingulate Gyrus	brain
7	chr3:133480000-133482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:133480000-133483800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:133480400-133486000	Genic enhancers	Brain Substantia Nigra	brain
10	chr3:133480800-133482400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:133480800-133482600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:133480800-133485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:133480800-133490000	Genic enhancers	HepG2	liver
14	chr3:133481200-133482400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:133481200-133482600	Strong transcription	Liver	Liver
16	chr3:133481200-133482800	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links