Variant report

Variant	rs17492375
Chromosome Location	chr4:124812897-124812898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10034152	0.80[EUR][1000 genomes]
rs1116266	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11732946	0.80[EUR][1000 genomes]
rs12639622	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648267	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13101469	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13109690	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116100	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1519242	0.80[EUR][1000 genomes]
rs2082502	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3097937	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3097939	0.84[ASN][1000 genomes]
rs34759155	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34845433	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35988830	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389113	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62321841	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62321845	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62321850	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6845345	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs986345	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv432623	chr4:124780908-124851395	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
3	nsv830049	chr4:124793932-124955708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17492375	SPATA5	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124794400-124813000	Weak transcription	Psoas Muscle	Psoas
2	chr4:124799400-124813200	Weak transcription	Fetal Heart	heart
3	chr4:124810600-124814800	Enhancers	NHDF-Ad	bronchial
4	chr4:124810800-124814400	Weak transcription	Left Ventricle	heart
5	chr4:124811000-124813000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:124811000-124814200	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:124811000-124814600	Weak transcription	Placenta	Placenta
8	chr4:124811200-124813600	Weak transcription	HepG2	liver
9	chr4:124811600-124813400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:124811600-124813600	Weak transcription	NHLF	lung
11	chr4:124812000-124814200	Enhancers	Fetal Lung	lung
12	chr4:124812000-124815200	Enhancers	Fetal Intestine Large	intestine
13	chr4:124812200-124816800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:124812400-124813000	Weak transcription	Fetal Stomach	stomach
15	chr4:124812400-124815000	Enhancers	Fetal Intestine Small	intestine
16	chr4:124812800-124813200	Enhancers	Esophagus	oesophagus
17	chr4:124812800-124813800	Enhancers	HUVEC	blood vessel
18	chr4:124812800-124814000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:124812800-124814800	Enhancers	Colon Smooth Muscle	Colon
20	chr4:124812800-124815400	Enhancers	Fetal Kidney	kidney

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