Variant report

Variant	rs1814880
Chromosome Location	chr15:79021140-79021141
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	FOXA1	chr15:79020745-79021184	HepG2	liver:	n/a	chr15:79020997-79021009
2	FOXA2	chr15:79020832-79021209	A549	lung:	n/a	chr15:79020997-79021009
3	FOXA2	chr15:79020889-79021155	A549	lung:	n/a	chr15:79020997-79021009

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79010822..79012780-chr15:79019538..79021262,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261303	TF binding region
CHRNB4	TF binding region
ENSG00000117971	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11072793	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11072794	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11072799	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11629639	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11629824	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11633170	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11634628	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11852887	0.89[EUR][1000 genomes]
rs11852909	0.93[EUR][1000 genomes]
rs11856441	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12899940	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901228	0.91[EUR][1000 genomes]
rs12904489	0.81[EUR][1000 genomes]
rs12906977	0.82[EUR][1000 genomes]
rs12907207	0.83[EUR][1000 genomes]
rs12907432	0.83[EUR][1000 genomes]
rs12907536	0.82[EUR][1000 genomes]
rs12913779	0.83[EUR][1000 genomes]
rs1383634	0.92[EUR][1000 genomes]
rs1383635	0.92[EUR][1000 genomes]
rs1809412	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1809414	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1809415	0.85[ASN][1000 genomes]
rs1825086	0.92[EUR][1000 genomes]
rs1904920	0.88[EUR][1000 genomes]
rs2017091	0.83[EUR][1000 genomes]
rs2219939	0.92[EUR][1000 genomes]
rs4887078	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58717592	0.83[ASN][1000 genomes]
rs62010554	0.82[ASN][1000 genomes]
rs71402966	0.81[EUR][1000 genomes]
rs755998	0.83[EUR][1000 genomes]
rs8030090	0.81[EUR][1000 genomes]
rs8030335	0.81[EUR][1000 genomes]
rs899997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9888691	0.90[AMR][1000 genomes];0.93[EUR][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1814880	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79019400-79022000	Enhancers	A549	lung
2	chr15:79019600-79021400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:79020200-79021200	Enhancers	Stomach Smooth Muscle	stomach
4	chr15:79020200-79021600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:79020200-79021600	Enhancers	Osteobl	bone
6	chr15:79020400-79021400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:79020400-79021400	Enhancers	Rectal Smooth Muscle	rectum
8	chr15:79020400-79022000	Enhancers	Colon Smooth Muscle	Colon
9	chr15:79020600-79021200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:79020800-79023000	Weak transcription	Fetal Stomach	stomach

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