Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr5:36587496-36587806	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000242292	TF binding region

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11743024	1.00[JPT][hapmap]
rs13154397	0.85[JPT][hapmap]
rs13155110	1.00[JPT][hapmap]
rs13178449	1.00[ASN][1000 genomes]
rs13179272	1.00[JPT][hapmap]
rs13186061	1.00[ASN][1000 genomes]
rs1366637	1.00[JPT][hapmap]
rs1549687	1.00[ASN][1000 genomes]
rs1549688	1.00[ASN][1000 genomes]
rs1549689	1.00[ASN][1000 genomes]
rs1972737	1.00[ASN][1000 genomes]
rs1972738	1.00[ASN][1000 genomes]
rs2562567	0.89[ASN][1000 genomes]
rs2731914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34000615	1.00[ASN][1000 genomes]
rs35016936	1.00[ASN][1000 genomes]
rs35678434	0.92[ASN][1000 genomes]
rs4421130	1.00[ASN][1000 genomes]
rs56011137	0.94[ASN][1000 genomes]
rs71588446	1.00[ASN][1000 genomes]
rs7445592	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881025	chr5:36575021-36613053	Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv830263	chr5:36576504-36755093	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv968166	chr5:36587211-36588834	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2731917	SLC1A3	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36584800-36590400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:36584800-36590800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:36585200-36590600	Weak transcription	Brain Anterior Caudate	brain
4	chr5:36585400-36590800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:36586200-36590600	Weak transcription	Brain Substantia Nigra	brain
6	chr5:36586200-36590800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:36587600-36587800	Enhancers	Left Ventricle	heart
8	chr5:36587600-36588000	Enhancers	Cortex derived primary cultured neurospheres	brain

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