Variant report

Variant	rs12766693
Chromosome Location	chr10:96058730-96058731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12255683	0.88[MEX][hapmap];0.88[TSI][hapmap]
rs12773803	0.81[EUR][1000 genomes]
rs12774398	0.84[EUR][1000 genomes]
rs12780240	0.81[AMR][1000 genomes]
rs12781422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781481	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12781628	0.83[EUR][1000 genomes]
rs12782263	1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12783744	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12783751	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1678	0.84[EUR][1000 genomes]
rs17438643	0.83[EUR][1000 genomes]
rs17438706	1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17439123	1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs17516758	0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17516904	1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17517368	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17517515	1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs17517578	0.89[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17517669	0.81[EUR][1000 genomes]
rs2274222	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs28478908	0.96[ASN][1000 genomes]
rs3203713	0.84[EUR][1000 genomes]
rs34053022	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34573359	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34999028	0.81[EUR][1000 genomes]
rs35058175	0.83[EUR][1000 genomes]
rs35084709	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35258481	0.85[EUR][1000 genomes]
rs35446195	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35658839	0.90[AMR][1000 genomes]
rs3758524	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs3758528	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs3818432	0.86[MKK][hapmap]
rs4394764	1.00[MEX][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs55666785	0.96[ASN][1000 genomes]
rs55980465	0.84[ASN][1000 genomes]
rs56041302	0.96[ASN][1000 genomes]
rs56041757	0.96[ASN][1000 genomes]
rs56141979	0.96[ASN][1000 genomes]
rs56240705	0.96[ASN][1000 genomes]
rs56376834	0.96[ASN][1000 genomes]
rs56400969	0.88[ASN][1000 genomes]
rs71480900	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71482303	0.81[EUR][1000 genomes]
rs71482304	0.81[EUR][1000 genomes]
rs71482305	0.81[EUR][1000 genomes]
rs730809	1.00[JPT][hapmap]
rs7914997	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[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	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12766693	NOC3L	cis	Heart Left Ventricle	GTEx
rs12766693	NOC3L	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96015000-96070200	Weak transcription	Fetal Brain Female	brain
2	chr10:96031800-96121000	Weak transcription	Stomach Mucosa	stomach
3	chr10:96035600-96066800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr10:96036000-96081600	Weak transcription	Left Ventricle	heart
5	chr10:96037800-96069000	Weak transcription	Gastric	stomach
6	chr10:96040200-96066200	Weak transcription	Pancreas	Pancrea
7	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
8	chr10:96045800-96061800	Weak transcription	Colonic Mucosa	Colon
9	chr10:96046200-96066200	Weak transcription	Right Atrium	heart
10	chr10:96047400-96060800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:96047800-96068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:96048800-96074800	Weak transcription	Placenta	Placenta
13	chr10:96049400-96081600	Weak transcription	Spleen	Spleen
14	chr10:96052800-96059000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr10:96052800-96073600	Weak transcription	Ovary	ovary
16	chr10:96053000-96059200	Weak transcription	HSMMtube	muscle
17	chr10:96053000-96068200	Weak transcription	Fetal Brain Male	brain
18	chr10:96053000-96083200	Weak transcription	Fetal Kidney	kidney
19	chr10:96053200-96081600	Weak transcription	Brain Substantia Nigra	brain
20	chr10:96053400-96059200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:96053400-96066200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:96053400-96069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:96053400-96073000	Weak transcription	Fetal Lung	lung
24	chr10:96055200-96074600	Strong transcription	Fetal Muscle Leg	muscle
25	chr10:96055600-96058800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:96056800-96061400	Strong transcription	Fetal Intestine Small	intestine
27	chr10:96057200-96062200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr10:96057200-96066800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:96057600-96060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:96057600-96060600	Strong transcription	Fetal Intestine Large	intestine
31	chr10:96057800-96062000	Strong transcription	Fetal Stomach	stomach
32	chr10:96058000-96060400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr10:96058000-96060600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr10:96058200-96059000	Strong transcription	Adipose Nuclei	Adipose
35	chr10:96058200-96059000	Strong transcription	Aorta	Aorta
36	chr10:96058200-96059800	Strong transcription	A549	lung
37	chr10:96058200-96060200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:96058200-96060200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:96058200-96060400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr10:96058200-96060400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr10:96058200-96060400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr10:96058400-96058800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr10:96058400-96058800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:96058400-96059400	Strong transcription	Brain Anterior Caudate	brain
45	chr10:96058400-96059600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:96058400-96059600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:96058400-96059800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:96058400-96060200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:96058400-96060200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:96058600-96058800	Bivalent Enhancer	Thymus	Thymus

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