Variant report

Variant	rs12769392
Chromosome Location	chr10:96269009-96269010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1048196	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1065027	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11187949	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11591693	0.84[EUR][1000 genomes]
rs11594492	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11595478	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11598738	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12569637	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12571306	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12571659	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766721	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12770064	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12774901	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12777300	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12783717	0.83[EUR][1000 genomes]
rs12785198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025445	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2031322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151952	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151953	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34151925	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34320768	0.88[EUR][1000 genomes]
rs34402112	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34560326	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35134124	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35602247	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35805353	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7082105	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[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	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12769392	CYP2C19	cis	Esophagus Mucosa	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96219800-96283400	Weak transcription	Lung	lung
3	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
4	chr10:96237600-96271400	Weak transcription	Placenta	Placenta
5	chr10:96238200-96273400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr10:96240200-96271000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:96244000-96282600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr10:96244400-96283600	Weak transcription	Pancreas	Pancrea
9	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
10	chr10:96248000-96273800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr10:96249200-96286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:96249400-96288600	Weak transcription	Gastric	stomach
13	chr10:96250400-96281000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:96250600-96271400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr10:96250800-96281000	Weak transcription	Brain Angular Gyrus	brain
16	chr10:96250800-96294000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:96250800-96297400	Weak transcription	Small Intestine	intestine
18	chr10:96251000-96271600	Weak transcription	Brain Substantia Nigra	brain
19	chr10:96256200-96271400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:96256200-96283600	Weak transcription	Osteobl	bone
21	chr10:96256400-96271400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:96256800-96271000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr10:96256800-96283800	Weak transcription	Liver	Liver
24	chr10:96257000-96293400	Weak transcription	HepG2	liver
25	chr10:96257200-96271000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:96259800-96271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:96260600-96269400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr10:96261000-96304400	Weak transcription	NH-A	brain
29	chr10:96263200-96271000	Weak transcription	Adipose Nuclei	Adipose
30	chr10:96264200-96296800	Weak transcription	Brain Germinal Matrix	brain
31	chr10:96266000-96304600	Weak transcription	Fetal Kidney	kidney
32	chr10:96266400-96269800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr10:96266800-96271800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr10:96266800-96274400	Strong transcription	HSMM	muscle
35	chr10:96267200-96269800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:96267400-96269200	ZNF genes & repeats	Fetal Stomach	stomach
37	chr10:96267400-96269400	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr10:96267400-96270600	Strong transcription	Left Ventricle	heart
39	chr10:96267400-96303800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:96267800-96280800	Weak transcription	Brain Anterior Caudate	brain
41	chr10:96268200-96283400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:96268400-96304400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr10:96268600-96269200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:96268600-96269400	Strong transcription	Colon Smooth Muscle	Colon
45	chr10:96268600-96269400	Strong transcription	Ovary	ovary
46	chr10:96268600-96269600	Strong transcription	Brain Hippocampus Middle	brain
47	chr10:96268600-96270000	Strong transcription	HSMMtube	muscle
48	chr10:96268600-96274000	Strong transcription	Fetal Intestine Large	intestine
49	chr10:96268600-96279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:96268800-96269400	Strong transcription	Fetal Muscle Leg	muscle

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