Variant report

Variant	rs12497453
Chromosome Location	chr3:121476618-121476619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121476465..121478394-chr3:121487558..121489191,2	K562	blood:
2	chr3:121468455..121470590-chr3:121475963..121478336,3	MCF-7	breast:
3	chr3:121467638..121471366-chr3:121473102..121477623,4	K562	blood:
4	chr3:121469866..121471508-chr3:121475985..121477623,2	K562	blood:
5	chr3:121467271..121469348-chr3:121476244..121478922,2	MCF-7	breast:
6	chr3:121475069..121477684-chr3:121478274..121481254,3	MCF-7	breast:
7	chr3:121476185..121478583-chr3:121487333..121489088,3	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10804555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492973	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920294	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2331963	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4234145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4259001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4431155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472078	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4505751	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4676757	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62268784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6438651	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767945	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776596	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7646523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12497453	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121469400-121489200	Weak transcription	Aorta	Aorta
2	chr3:121469400-121489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:121475400-121477200	Enhancers	Fetal Muscle Trunk	muscle
4	chr3:121475400-121477400	Enhancers	Ovary	ovary
5	chr3:121475800-121477000	Enhancers	HSMM	muscle
6	chr3:121475800-121477400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:121475800-121478000	Enhancers	HepG2	liver
8	chr3:121475800-121479200	Enhancers	HSMMtube	muscle
9	chr3:121476000-121477200	Enhancers	K562	blood
10	chr3:121476200-121476800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:121476400-121476800	Enhancers	Dnd41	blood
12	chr3:121476400-121477000	Enhancers	Placenta	Placenta
13	chr3:121476400-121477200	Enhancers	Left Ventricle	heart
14	chr3:121476400-121477400	Enhancers	Fetal Heart	heart
15	chr3:121476600-121476800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:121476600-121477200	Enhancers	Right Atrium	heart
17	chr3:121476600-121485600	Weak transcription	Primary B cells from cord blood	blood

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