Variant report

Variant	rs725089
Chromosome Location	chr3:56503046-56503047
allele	C/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	chr3:56503036-56503104	Gliobla	brain:	n/a	n/a
2	REST	chr3:56501014-56503103	H1-neurons	neurons:	n/a	chr3:56502285-56502298
3	CTCF	chr3:56502127-56503167	SK-N-SH	brain:	n/a	chr3:56502745-56502761 chr3:56502239-56502252 chr3:56502744-56502762 chr3:56502746-56502759 chr3:56502699-56502712
4	E2F4	chr3:56502937-56503137	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ERC2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1388255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1491163	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552668	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1552669	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878269	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35139577	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4527348	0.98[EUR][1000 genomes]
rs4974214	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58145335	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6445790	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445792	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6762660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6784781	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785094	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6796830	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807444	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7628279	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637479	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7644198	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7646515	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs975582	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9812701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829542	0.94[EUR][1000 genomes]
rs9856358	0.94[EUR][1000 genomes]
rs9871408	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs725089	ERC2	cis	cerebellum	SCAN
rs725089	C3orf51	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56500600-56503200	Active TSS	Brain Cingulate Gyrus	brain
2	chr3:56500600-56503200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:56500600-56503200	Active TSS	Fetal Brain Female	brain
4	chr3:56500800-56503200	Active TSS	Brain Anterior Caudate	brain
5	chr3:56501400-56503200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:56502400-56503200	Bivalent Enhancer	Placenta	Placenta
7	chr3:56502400-56510800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:56502600-56503200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:56502800-56503200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:56502800-56503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:56502800-56503200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
12	chr3:56503000-56503200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:56503000-56503200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:56503000-56503200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
15	chr3:56503000-56503200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:56503000-56503200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:56503000-56503200	Bivalent Enhancer	Fetal Brain Male	brain
18	chr3:56503000-56503400	Enhancers	NH-A	brain
19	chr3:56503000-56503600	Enhancers	HUVEC	blood vessel

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