Variant report

Variant	rs12475377
Chromosome Location	chr2:134490796-134490797
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134488907..134491091-chr20:55839209..55841461,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10496709	0.82[EUR][1000 genomes]
rs12465737	0.85[EUR][1000 genomes]
rs12467346	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12472423	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1446748	0.82[EUR][1000 genomes]
rs1446749	0.83[EUR][1000 genomes]
rs1470510	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1562349	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16828705	0.82[EUR][1000 genomes]
rs16828728	0.82[EUR][1000 genomes]
rs1867894	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992783	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992784	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4369917	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4369918	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55715603	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55932202	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56111185	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56341649	0.82[EUR][1000 genomes]
rs58457553	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6706052	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72843245	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72843247	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72843252	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72843260	0.83[EUR][1000 genomes]
rs72843263	0.83[EUR][1000 genomes]
rs921087	0.84[EUR][1000 genomes];0.81[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	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134485000-134492400	Weak transcription	Right Atrium	heart
2	chr2:134485200-134490800	Weak transcription	NHDF-Ad	bronchial
3	chr2:134490600-134491200	Enhancers	Fetal Muscle Leg	muscle
4	chr2:134490600-134491400	Enhancers	Brain Hippocampus Middle	brain
5	chr2:134490600-134492800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:134490600-134493000	Enhancers	Osteobl	bone
7	chr2:134490600-134493400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links