Variant report

Variant	rs9669474
Chromosome Location	chr12:118509347-118509348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11610878	0.81[EUR][1000 genomes]
rs11613924	0.91[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12809627	1.00[EUR][1000 genomes]
rs35298010	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55833872	0.97[ASN][1000 genomes]
rs7134851	0.94[ASN][1000 genomes]
rs7486601	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7488596	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7489079	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9668653	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9669474	TAOK3	cis	cerebellum	SCAN
rs9669474	C12orf49	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118500400-118515400	Weak transcription	Gastric	stomach
2	chr12:118500400-118516800	Weak transcription	Spleen	Spleen
3	chr12:118500600-118535200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:118500800-118511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:118500800-118515400	Weak transcription	Esophagus	oesophagus
6	chr12:118500800-118518200	Weak transcription	Left Ventricle	heart
7	chr12:118500800-118526400	Weak transcription	HMEC	breast
8	chr12:118500800-118539600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:118500800-118539800	Weak transcription	Right Ventricle	heart
10	chr12:118500800-118540800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:118501000-118514400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:118501000-118515000	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:118501000-118515200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:118501000-118515400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:118501000-118515400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:118501000-118516400	Weak transcription	Colonic Mucosa	Colon
17	chr12:118501000-118517200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:118501000-118525600	Weak transcription	Fetal Brain Female	brain
19	chr12:118501000-118527400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:118501000-118530600	Weak transcription	Brain Angular Gyrus	brain
21	chr12:118501000-118533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:118501000-118539600	Weak transcription	Psoas Muscle	Psoas
23	chr12:118501000-118540200	Weak transcription	HUVEC	blood vessel
24	chr12:118501000-118540800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:118501000-118540800	Weak transcription	NH-A	brain
26	chr12:118501200-118510400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:118501200-118511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:118501200-118511400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:118501200-118514400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:118501200-118515400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:118501200-118516200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:118501200-118526400	Weak transcription	Small Intestine	intestine
33	chr12:118501200-118536000	Weak transcription	Right Atrium	heart
34	chr12:118501200-118540400	Weak transcription	Brain Germinal Matrix	brain
35	chr12:118501200-118540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:118501200-118541000	Weak transcription	Aorta	Aorta
37	chr12:118501400-118510400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:118501600-118519800	Weak transcription	Fetal Brain Male	brain
39	chr12:118501600-118540400	Weak transcription	NHLF	lung
40	chr12:118501800-118511400	Weak transcription	Pancreas	Pancrea
41	chr12:118501800-118511800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:118501800-118527000	Weak transcription	NHEK	skin
43	chr12:118501800-118533200	Weak transcription	Hela-S3	cervix
44	chr12:118502000-118515400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:118502000-118515600	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:118502200-118511000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:118502200-118515200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:118502200-118540800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:118502200-118540800	Weak transcription	Brain Anterior Caudate	brain
50	chr12:118502400-118515400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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