Variant report

Variant	rs9785225
Chromosome Location	chr9:93982492-93982493
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:9)

rs_ID	r²[population]
rs10820842	0.85[EUR][1000 genomes]
rs10991823	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10991829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991891	1.00[CEU][hapmap]
rs10991899	0.89[CEU][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes]
rs6479333	0.89[CEU][hapmap]
rs7045608	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7047354	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9785224	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:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893570	chr9:93973938-94148084	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS 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	9 gene(s)	inside rSNPs	diseases
2	nsv482877	chr9:93979351-94157734	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9785225	FGD3	cis	parietal	SCAN
rs9785225	FAM120A	cis	parietal	SCAN
rs9785225	CENPP	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93970200-93984000	Weak transcription	K562	blood
2	chr9:93970400-94005400	Weak transcription	Aorta	Aorta
3	chr9:93970800-93983600	Weak transcription	Brain Substantia Nigra	brain
4	chr9:93970800-93983800	Weak transcription	Brain Angular Gyrus	brain
5	chr9:93970800-93984200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:93970800-93985200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:93971000-93983200	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:93971000-93984200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:93971000-94007800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:93971200-93983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:93971400-93982800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:93971400-93983800	Weak transcription	Dnd41	blood
13	chr9:93971400-93984200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:93971400-93984400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:93971400-94009400	Weak transcription	Spleen	Spleen
16	chr9:93971600-93982600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:93971600-93983200	Weak transcription	Brain Anterior Caudate	brain
18	chr9:93971600-93983800	Weak transcription	Psoas Muscle	Psoas
19	chr9:93971800-94008000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr9:93972800-94009200	Weak transcription	Brain Germinal Matrix	brain
21	chr9:93973000-93984000	Weak transcription	Fetal Brain Male	brain
22	chr9:93973000-93984600	Weak transcription	Small Intestine	intestine
23	chr9:93973600-93982600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:93973600-93995800	Weak transcription	Fetal Brain Female	brain
25	chr9:93974600-93982800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:93974800-93983400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:93974800-93983800	Weak transcription	A549	lung
28	chr9:93975000-93982600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:93975000-93983800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:93975200-93983000	Weak transcription	Colonic Mucosa	Colon
31	chr9:93975400-93985000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:93975800-93983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:93975800-94005000	Weak transcription	Fetal Kidney	kidney
34	chr9:93976000-94002000	Weak transcription	Gastric	stomach
35	chr9:93976800-93982600	Weak transcription	HepG2	liver
36	chr9:93977000-93983800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:93977200-93984400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:93977400-93983000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:93977400-93985400	Weak transcription	Hela-S3	cervix
40	chr9:93977600-93982800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:93977600-93983800	Weak transcription	NHLF	lung
42	chr9:93978600-93982800	Strong transcription	Left Ventricle	heart
43	chr9:93979200-93982600	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:93979200-93983000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr9:93979200-93995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:93979600-93983200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr9:93979800-93983200	Strong transcription	Liver	Liver
48	chr9:93979800-93984000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:93979800-93984400	Strong transcription	Primary T cells from cord blood	blood
50	chr9:93980000-93982800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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