Variant report

Variant	rs12901624
Chromosome Location	chr15:77988578-77988579
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	TCF7L2	chr15:77988307-77988858	HCT-116	colon:	n/a	chr15:77988641-77988651 chr15:77988641-77988650 chr15:77988637-77988653 chr15:77988638-77988652 chr15:77988637-77988653
2	NFIC	chr15:77988458-77989085	ECC-1	luminal epithelium:	n/a	n/a
3	TCF7L2	chr15:77988517-77988862	Hela-S3	cervix:	n/a	chr15:77988641-77988651 chr15:77988641-77988650 chr15:77988637-77988653 chr15:77988638-77988652 chr15:77988637-77988653

Variant related genes	Relation type
LINGO1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11631120	0.82[ASN][1000 genomes]
rs11638112	0.82[ASN][1000 genomes]
rs11638387	0.85[ASN][1000 genomes]
rs12900699	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901113	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901420	0.85[ASN][1000 genomes]
rs12905478	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906523	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907043	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914049	0.85[ASN][1000 genomes]
rs12914780	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164838	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440622	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34464560	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34520587	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35091811	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35353380	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35390302	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35409437	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971971	0.85[ASN][1000 genomes]
rs36078248	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66744051	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66951253	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67818419	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67965873	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	chr15:77987600-77988800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr15:77987600-77989200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
7	chr15:77987600-77989200	Enhancers	Fetal Brain Male	brain
8	chr15:77987600-77989400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr15:77987800-77988600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
10	chr15:77987800-77989000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:77987800-77989000	Enhancers	Ovary	ovary
12	chr15:77987800-77989200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr15:77987800-77989600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr15:77988000-77989000	Bivalent Enhancer	Placenta	Placenta
15	chr15:77988000-77989200	Bivalent Enhancer	Fetal Stomach	stomach
16	chr15:77988000-77989800	Enhancers	Spleen	Spleen
17	chr15:77988200-77988600	Enhancers	Brain Angular Gyrus	brain
18	chr15:77988200-77989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:77988400-77988600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:77988400-77988600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:77988400-77988800	Enhancers	Brain Anterior Caudate	brain
22	chr15:77988400-77988800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr15:77988400-77989000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:77988400-77989000	Bivalent Enhancer	Fetal Brain Female	brain
25	chr15:77988400-77989000	Enhancers	Fetal Lung	lung
26	chr15:77988400-77989200	Enhancers	Fetal Heart	heart
27	chr15:77988400-77989400	Bivalent Enhancer	Brain Hippocampus Middle	brain

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