Variant report

Variant	rs17250623
Chromosome Location	chr9:108394893-108394894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1018847	1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs10491808	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12115847	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs17251166	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17308339	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17309137	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17309319	0.94[EUR][1000 genomes]
rs17309806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068267	0.87[EUR][1000 genomes]
rs2771028	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2771039	0.90[EUR][1000 genomes]
rs2771044	0.90[EUR][1000 genomes]
rs2771045	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2812299	0.81[EUR][1000 genomes]
rs2812300	0.81[EUR][1000 genomes]
rs2812301	0.85[EUR][1000 genomes]
rs2812302	0.81[EUR][1000 genomes]
rs2812306	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2812309	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2812311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs2812312	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs34787999	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41277785	0.88[EUR][1000 genomes]
rs4742649	0.87[EUR][1000 genomes]
rs4742651	0.92[EUR][1000 genomes]
rs4742653	0.88[EUR][1000 genomes]
rs4742654	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4742946	0.86[EUR][1000 genomes]
rs4742949	0.87[EUR][1000 genomes]
rs4742950	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4742952	0.88[EUR][1000 genomes]
rs4742953	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4742954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742955	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57432946	0.92[EUR][1000 genomes]
rs57597571	0.88[EUR][1000 genomes]
rs59474306	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60126815	0.81[EUR][1000 genomes]
rs62575093	0.85[EUR][1000 genomes]
rs62575095	0.90[EUR][1000 genomes]
rs62575101	0.87[EUR][1000 genomes]
rs62575102	0.87[EUR][1000 genomes]
rs62575104	0.91[EUR][1000 genomes]
rs62575105	0.87[EUR][1000 genomes]
rs62575106	0.91[EUR][1000 genomes]
rs62575112	0.83[EUR][1000 genomes]
rs62575114	0.91[EUR][1000 genomes]
rs62575144	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575145	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024265	0.95[EUR][1000 genomes]
rs7035783	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7037972	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7851777	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7872377	0.86[EUR][1000 genomes]
rs9408799	0.86[EUR][1000 genomes]
rs9409062	0.86[EUR][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	nsv519023	chr9:108371549-108454745	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17250623	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:108333200-108400400	Weak transcription	HMEC	breast
3	chr9:108335400-108403400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:108338400-108403400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:108345600-108400000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:108347000-108399600	Weak transcription	Psoas Muscle	Psoas
7	chr9:108349400-108402200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108350800-108403800	Weak transcription	Fetal Heart	heart
9	chr9:108354400-108395800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:108354400-108395800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:108354400-108397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:108354400-108397400	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
16	chr9:108354600-108395600	Weak transcription	Brain Angular Gyrus	brain
17	chr9:108354600-108397000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:108354600-108397200	Weak transcription	Aorta	Aorta
19	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
20	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:108354800-108396400	Weak transcription	Fetal Stomach	stomach
22	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
23	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:108355800-108396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:108355800-108397200	Weak transcription	Ovary	ovary
26	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
27	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
28	chr9:108359800-108397000	Weak transcription	Liver	Liver
29	chr9:108360600-108397000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:108361000-108397200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:108366800-108396800	Weak transcription	NHDF-Ad	bronchial
32	chr9:108366800-108397000	Weak transcription	Dnd41	blood
33	chr9:108366800-108397200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:108366800-108418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:108366800-108418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:108367200-108396200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:108367200-108396800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:108367200-108399600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:108367200-108399600	Weak transcription	Fetal Intestine Large	intestine
43	chr9:108367200-108402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:108367200-108403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:108367400-108396800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:108367400-108407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:108371200-108395000	Weak transcription	Left Ventricle	heart
48	chr9:108372200-108402200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:108373000-108397000	Weak transcription	Lung	lung
50	chr9:108373200-108398800	Weak transcription	Fetal Muscle Trunk	muscle

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