Variant report

Variant	rs10509690
Chromosome Location	chr10:97246036-97246037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11595114	1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[ASN][1000 genomes]
rs12414693	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12415079	0.83[ASN][1000 genomes]
rs12415681	0.83[ASN][1000 genomes]
rs12416103	1.00[JPT][hapmap]
rs45572141	0.87[AMR][1000 genomes]
rs4918940	0.95[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap]
rs55941659	0.87[AMR][1000 genomes]
rs61868706	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045002	chr10:97214418-97250630	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10509690	FRAT2	cis	cerebellum	SCAN
rs10509690	C10orf62	cis	parietal	SCAN
rs10509690	CYP2C8	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97237200-97254000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:97239600-97260800	Weak transcription	Brain Germinal Matrix	brain
3	chr10:97240600-97253000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:97240800-97248800	Weak transcription	Fetal Brain Female	brain
5	chr10:97240800-97253400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:97241000-97247200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:97241000-97260600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:97241400-97253600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:97241600-97246800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr10:97241600-97254000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:97241600-97260400	Weak transcription	Fetal Brain Male	brain
12	chr10:97241600-97260600	Weak transcription	Fetal Stomach	stomach
13	chr10:97241800-97249200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr10:97241800-97256400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:97242000-97253800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:97242000-97256400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:97242600-97247200	Weak transcription	Psoas Muscle	Psoas
18	chr10:97242600-97248200	Weak transcription	Fetal Heart	heart
19	chr10:97242600-97252200	Weak transcription	Pancreas	Pancrea
20	chr10:97242800-97247200	Weak transcription	Liver	Liver
21	chr10:97242800-97256000	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:97243000-97247000	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:97243000-97253400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:97244000-97246200	Enhancers	Brain Anterior Caudate	brain
25	chr10:97244200-97253200	Weak transcription	Lung	lung
26	chr10:97244600-97246200	Enhancers	Brain Cingulate Gyrus	brain
27	chr10:97244600-97246400	Enhancers	HSMMtube	muscle
28	chr10:97244800-97246400	Enhancers	Rectal Smooth Muscle	rectum
29	chr10:97244800-97246600	Weak transcription	Placenta	Placenta
30	chr10:97244800-97247000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:97244800-97247200	Weak transcription	Fetal Intestine Small	intestine
32	chr10:97245000-97246200	Enhancers	Brain Hippocampus Middle	brain
33	chr10:97245200-97246200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr10:97245200-97249200	Weak transcription	Fetal Intestine Large	intestine
35	chr10:97245200-97249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr10:97245200-97251000	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr10:97245200-97252200	Weak transcription	Gastric	stomach
38	chr10:97245400-97250400	Weak transcription	Stomach Mucosa	stomach
39	chr10:97245400-97252400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr10:97245400-97259200	Weak transcription	Brain Substantia Nigra	brain
41	chr10:97245400-97264600	Weak transcription	Ovary	ovary
42	chr10:97245600-97246200	Enhancers	Right Atrium	heart
43	chr10:97245600-97247000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:97245800-97247200	Weak transcription	HSMM	muscle
45	chr10:97245800-97250600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr10:97245800-97254000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:97245800-97259400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:97246000-97246200	Enhancers	Fetal Lung	lung
49	chr10:97246000-97247000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:97246000-97247000	Weak transcription	Brain Angular Gyrus	brain

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