Variant report

Variant	rs12590844
Chromosome Location	chr14:38259876-38259877
allele	A/G
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	FOXA2	chr14:38259595-38262168	HepG2	liver:	n/a	chr14:38260697-38260709

Variant related genes	Relation type
TTC6	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11849079	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587895	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17107096	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107102	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17107141	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1951645	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs1952784	0.81[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs1957584	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs1980680	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs2415414	0.88[EUR][1000 genomes]
rs4901272	0.81[GIH][hapmap]
rs4901274	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs55712036	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58878623	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59262826	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61977158	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496750	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66617416	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67863208	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010511	0.89[EUR][1000 genomes]
rs8011077	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs8012810	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs969446	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv564383	chr14:38223275-38262762	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv564384	chr14:38233493-38262762	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv564385	chr14:38246440-38321607	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38259400-38261600	Enhancers	HepG2	liver
2	chr14:38259600-38260000	Weak transcription	Fetal Intestine Small	intestine

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