Variant report

Variant	rs73465808
Chromosome Location	chr15:77988912-77988913
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	NFIC	chr15:77988458-77989085	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
LINGO1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs56314140	1.00[AMR][1000 genomes]
rs56343471	1.00[AMR][1000 genomes]
rs56844012	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56952924	1.00[AMR][1000 genomes]
rs57548921	1.00[AMR][1000 genomes]
rs57594261	1.00[AMR][1000 genomes]
rs57603227	1.00[AMR][1000 genomes]
rs58398016	1.00[AMR][1000 genomes]
rs58469778	1.00[AMR][1000 genomes]
rs58711165	1.00[AMR][1000 genomes]
rs58768836	1.00[AMR][1000 genomes]
rs58838783	1.00[AMR][1000 genomes]
rs59287349	1.00[AMR][1000 genomes]
rs59391272	1.00[AMR][1000 genomes]
rs59912838	1.00[AMR][1000 genomes]
rs60096962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60602435	1.00[AMR][1000 genomes]
rs60706078	1.00[AMR][1000 genomes]
rs60973601	1.00[AMR][1000 genomes]
rs73455712	1.00[AMR][1000 genomes]
rs73455720	1.00[AMR][1000 genomes]
rs73455780	1.00[AMR][1000 genomes]
rs73455799	1.00[AMR][1000 genomes]
rs73457716	1.00[AMR][1000 genomes]
rs73457852	1.00[AMR][1000 genomes]
rs73457862	1.00[AMR][1000 genomes]
rs73457865	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73465815	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73465817	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73465837	1.00[AMR][1000 genomes]
rs73465849	1.00[AMR][1000 genomes]
rs73465855	1.00[AMR][1000 genomes]
rs73465863	1.00[AMR][1000 genomes]
rs74025336	1.00[AMR][1000 genomes]
rs74025396	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv570141	chr15:77985554-78017361	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77969200-78007600	Weak transcription	Right Atrium	heart
2	chr15:77980400-77989800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:77985200-77990200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:77986800-77989200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:77987600-77989200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
6	chr15:77987600-77989200	Enhancers	Fetal Brain Male	brain
7	chr15:77987600-77989400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr15:77987800-77989000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:77987800-77989000	Enhancers	Ovary	ovary
10	chr15:77987800-77989200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr15:77987800-77989600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr15:77988000-77989000	Bivalent Enhancer	Placenta	Placenta
13	chr15:77988000-77989200	Bivalent Enhancer	Fetal Stomach	stomach
14	chr15:77988000-77989800	Enhancers	Spleen	Spleen
15	chr15:77988200-77989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:77988400-77989000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:77988400-77989000	Bivalent Enhancer	Fetal Brain Female	brain
18	chr15:77988400-77989000	Enhancers	Fetal Lung	lung
19	chr15:77988400-77989200	Enhancers	Fetal Heart	heart
20	chr15:77988400-77989400	Bivalent Enhancer	Brain Hippocampus Middle	brain
21	chr15:77988600-77989000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:77988600-77989400	Weak transcription	Brain Angular Gyrus	brain
23	chr15:77988600-77991800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:77988800-77989000	Bivalent Enhancer	Brain Germinal Matrix	brain
25	chr15:77988800-77989000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
26	chr15:77988800-77989000	Bivalent Enhancer	Hela-S3	cervix
27	chr15:77988800-77989400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain

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