Variant report

Variant	rs2812309
Chromosome Location	chr9:108236362-108236363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108236271..108237862-chr9:108239402..108241098,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1018847	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10491808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12115847	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17250623	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17251166	0.91[CEU][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs17308339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17309137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17309319	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17309806	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs2068267	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2771028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771037	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2771039	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771044	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771045	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812298	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812299	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812301	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812302	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812304	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812306	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2812311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2812312	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34787999	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41277785	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4742649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742651	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4742653	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742654	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4742946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742949	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4742950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4742952	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4742954	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742955	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs4742956	0.91[CEU][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs57432946	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57597571	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59474306	0.84[EUR][1000 genomes]
rs60126815	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575093	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62575095	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575102	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62575104	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62575105	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62575106	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62575112	0.83[EUR][1000 genomes]
rs62575114	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62575144	0.88[EUR][1000 genomes]
rs62575145	0.89[EUR][1000 genomes]
rs7024265	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7035783	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7037972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7851777	0.96[CEU][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7872377	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs885954	0.86[YRI][hapmap]
rs9408799	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409062	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2812309	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
3	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
5	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
7	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
10	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
11	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
13	chr9:108221000-108266000	Weak transcription	NHEK	skin
14	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
15	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
16	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
19	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:108222200-108277000	Weak transcription	Ovary	ovary
21	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
23	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
24	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
25	chr9:108223200-108252600	Weak transcription	K562	blood
26	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
28	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr9:108227800-108239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr9:108228200-108237400	Weak transcription	Liver	Liver
35	chr9:108228200-108237600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:108228200-108250200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:108228400-108238600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:108228400-108252400	Weak transcription	Fetal Intestine Large	intestine
39	chr9:108228400-108257600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:108230200-108236400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:108231400-108250200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:108231400-108257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:108231600-108249800	Weak transcription	NHLF	lung
44	chr9:108231800-108237400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:108231800-108247000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:108231800-108254400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:108232000-108236400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:108232000-108252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr9:108232200-108246800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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