Variant report

Variant	rs16840812
Chromosome Location	chr3:133462807-133462808
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	FOXA2	chr3:133460833-133462885	HepG2	liver:	n/a	chr3:133461892-133461904 chr3:133461582-133461594

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133379775..133382913-chr3:133460288..133462996,3	MCF-7	breast:
2	chr3:133460249..133463891-chr3:133464263..133466995,3	MCF-7	breast:

Variant related genes	Relation type
TF	TF binding region
ENSG00000091513	Chromatin interaction
ENSG00000163781	Chromatin interaction
ENSG00000242337	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10049093	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10935081	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10935083	0.91[ASN][1000 genomes]
rs11715340	0.87[ASN][1000 genomes]
rs11717407	0.88[ASN][1000 genomes]
rs16840692	0.84[ASN][1000 genomes]
rs16840699	0.88[ASN][1000 genomes]
rs16840751	0.89[ASN][1000 genomes]
rs1799852	0.82[JPT][hapmap]
rs4241356	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4428180	0.94[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532136	0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4582061	0.88[ASN][1000 genomes]
rs4854595	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4854748	0.97[ASN][1000 genomes]
rs4854749	0.97[ASN][1000 genomes]
rs4854750	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4854752	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4854754	0.89[ASN][1000 genomes]
rs4854755	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4854757	0.91[ASN][1000 genomes]
rs6801244	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8177181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177184	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]
rs8177185	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8177186	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8177203	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs8177215	0.82[JPT][hapmap]
rs9714237	0.84[ASN][1000 genomes]
rs9847885	0.88[ASN][1000 genomes]

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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133460400-133464600	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr3:133460800-133464600	Enhancers	Brain Angular Gyrus	brain
3	chr3:133461600-133464400	Enhancers	Brain Cingulate Gyrus	brain
4	chr3:133461600-133464400	Enhancers	Brain Substantia Nigra	brain
5	chr3:133461800-133463400	Flanking Active TSS	HepG2	liver
6	chr3:133461800-133464400	Enhancers	Brain Hippocampus Middle	brain
7	chr3:133461800-133464600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:133462000-133464600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:133462200-133463600	Weak transcription	K562	blood
10	chr3:133462200-133464400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:133462200-133464400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:133462400-133464400	Enhancers	Brain Anterior Caudate	brain
13	chr3:133462600-133463400	Enhancers	Liver	Liver
14	chr3:133462800-133463600	Enhancers	Spleen	Spleen
15	chr3:133462800-133464400	Weak transcription	Pancreas	Pancrea

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