Variant report

Variant	rs12472151
Chromosome Location	chr2:234852692-234852693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234683624-234705119..2:234843685-234852750	Hela-S3	cervix:
2	2:234543708-234558325..2:234843685-234852750	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000234143	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000242515	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10166496	1.00[CEU][hapmap]
rs10169266	1.00[CEU][hapmap]
rs11563102	1.00[LWK][hapmap]
rs11563211	1.00[CEU][hapmap]
rs12470426	1.00[CHB][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12473889	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs12992084	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020968	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];1.00[ASN][1000 genomes]
rs13024825	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17862921	0.82[CHB][hapmap]
rs17863838	0.82[CHB][hapmap]
rs17863841	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs17863842	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs17863848	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17864749	0.97[EUR][1000 genomes]
rs17868384	0.97[ASN][1000 genomes]
rs17868387	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28946910	1.00[CEU][hapmap]
rs28946912	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28948671	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs34032602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123979	0.97[EUR][1000 genomes]
rs66567403	0.90[EUR][1000 genomes]
rs6741751	0.82[CHB][hapmap]
rs67646620	0.97[ASN][1000 genomes]
rs7562952	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.95[ASN][1000 genomes]
rs7562971	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs7593557	1.00[CEU][hapmap]
rs9646718	0.82[CHB][hapmap]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876024	chr2:234842650-234856421	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Alcohol consumption	23942779	GWAS catalog

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234848000-234852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:234849400-234883400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:234849600-234873800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:234851600-234854000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:234852200-234852800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:234852400-234853000	ZNF genes & repeats	Primary T cells from cord blood	blood

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