Variant report

Variant	rs12473889
Chromosome Location	chr2:234844945-234844946
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: 0)

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

rs_ID	r²[population]
rs1004478	0.93[CEU][hapmap]
rs10490010	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10803665	1.00[CEU][hapmap]
rs10803666	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11562954	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12470426	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472151	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs12992084	0.83[ASN][1000 genomes]
rs13004520	0.97[ASN][1000 genomes]
rs13020968	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs13028228	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17862920	0.93[CEU][hapmap]
rs17862921	0.86[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[MKK][hapmap]
rs17863838	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs17863841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17863842	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]
rs17863848	0.83[ASN][1000 genomes]
rs17864741	0.93[CEU][hapmap]
rs17868384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17868387	0.83[ASN][1000 genomes]
rs28946912	0.83[ASN][1000 genomes]
rs34032602	0.97[ASN][1000 genomes]
rs35168608	0.82[ASN][1000 genomes]
rs6741751	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs67646620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558436	1.00[CEU][hapmap]
rs7562952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7577262	0.93[CEU][hapmap]
rs9646718	0.93[CEU][hapmap];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

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234841800-234847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:234843000-234845400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:234844400-234845200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:234844800-234845400	Enhancers	Cortex derived primary cultured neurospheres	brain

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