Variant report

Variant	rs57597571
Chromosome Location	chr9:108299190-108299191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1018847	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10491808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12115847	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17250623	0.88[EUR][1000 genomes]
rs17251166	0.86[EUR][1000 genomes]
rs17308339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17309137	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17309319	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17309806	0.91[EUR][1000 genomes]
rs2068267	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771028	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2771037	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2771039	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2771044	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2771045	0.97[AMR][1000 genomes];0.93[EUR][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];0.88[ASN][1000 genomes]
rs2812300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812301	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812302	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812304	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812306	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812309	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2812311	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812312	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34787999	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41277785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742649	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742651	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742653	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742654	0.85[EUR][1000 genomes]
rs4742946	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4742949	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742952	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742953	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742954	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742955	0.89[EUR][1000 genomes]
rs4742956	0.91[EUR][1000 genomes]
rs57432946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59474306	0.87[EUR][1000 genomes]
rs60126815	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575093	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575095	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575102	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575104	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575112	0.85[EUR][1000 genomes]
rs62575114	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575144	0.90[EUR][1000 genomes]
rs62575145	0.91[EUR][1000 genomes]
rs7024265	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7035783	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037972	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851777	0.88[EUR][1000 genomes]
rs7872377	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9408799	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9409062	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[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	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
2	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
3	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
4	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	nsv416298	chr9:108295722-108303569	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57597571	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
4	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
5	chr9:108272800-108304600	Weak transcription	NHEK	skin
6	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
7	chr9:108276200-108309200	Weak transcription	Lung	lung
8	chr9:108278800-108305800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:108279000-108311400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:108282400-108299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:108282400-108300000	Weak transcription	HSMMtube	muscle
14	chr9:108282400-108302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:108282400-108302800	Weak transcription	HSMM	muscle
16	chr9:108282400-108312400	Weak transcription	HepG2	liver
17	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
19	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
20	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:108289200-108306200	Weak transcription	Fetal Brain Male	brain
22	chr9:108289800-108309800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:108291800-108310200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:108292600-108305600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:108292600-108319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:108293600-108299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:108293800-108319800	Weak transcription	Liver	Liver
28	chr9:108294400-108304400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:108294600-108299600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr9:108294600-108305200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:108294800-108312000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:108294800-108319800	Weak transcription	Hela-S3	cervix
33	chr9:108295600-108305800	Weak transcription	Brain Germinal Matrix	brain
34	chr9:108295600-108305800	Weak transcription	Fetal Intestine Large	intestine
35	chr9:108295600-108319800	Weak transcription	Aorta	Aorta
36	chr9:108296200-108302000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:108296200-108303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:108296400-108299200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:108296400-108316200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:108297000-108301200	Weak transcription	Osteobl	bone
41	chr9:108297200-108311800	Weak transcription	Fetal Muscle Leg	muscle
42	chr9:108297600-108306000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:108297600-108309200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:108297600-108311600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:108297600-108319800	Weak transcription	NHLF	lung
46	chr9:108297800-108300000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:108297800-108302800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:108297800-108319200	Weak transcription	Dnd41	blood
49	chr9:108297800-108319800	Weak transcription	Adipose Nuclei	Adipose
50	chr9:108298000-108319800	Weak transcription	NHDF-Ad	bronchial

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