Variant report

Variant	rs3923209
Chromosome Location	chr5:151937593-151937594
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10036750	0.80[EUR][1000 genomes]
rs10045463	0.80[EUR][1000 genomes]
rs10155517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515675	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10515676	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11167584	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11956651	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12188564	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13359939	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13361438	0.87[ASN][1000 genomes]
rs17452991	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453481	0.88[EUR][1000 genomes]
rs17453530	0.88[EUR][1000 genomes]
rs17453740	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17453775	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454420	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17549488	0.81[EUR][1000 genomes]
rs17550343	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17565365	0.95[ASN][1000 genomes]
rs17565693	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2961741	0.81[EUR][1000 genomes]
rs2961756	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961760	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961765	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961766	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964223	0.83[EUR][1000 genomes]
rs2964230	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964231	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246033	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4398624	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4406125	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4478308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484412	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4557395	0.87[EUR][1000 genomes]
rs4580766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958316	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958317	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958320	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958323	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958537	1.00[JPT][hapmap]
rs4958560	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958561	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958562	0.87[EUR][1000 genomes]
rs4958564	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958566	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958567	0.82[EUR][1000 genomes]
rs4958568	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958569	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55648729	0.83[EUR][1000 genomes]
rs55786399	0.88[EUR][1000 genomes]
rs56014830	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67979431	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871699	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6876403	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6876723	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884556	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6895969	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795364	0.81[EUR][1000 genomes]
rs72795366	0.80[EUR][1000 genomes]
rs72795376	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795379	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795389	0.88[EUR][1000 genomes]
rs72797226	0.95[ASN][1000 genomes]
rs72797233	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797237	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797243	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797251	0.83[EUR][1000 genomes]
rs72797254	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797262	0.83[EUR][1000 genomes]
rs72797296	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72799113	0.95[ASN][1000 genomes]
rs9324734	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs982716	1.00[JPT][hapmap]

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	nsv1023828	chr5:151522149-151956217	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3923209	GLRA1	cis	cerebellum	SCAN
rs3923209	SLC26A2	cis	cerebellum	SCAN
rs3923209	GALNTL2	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151934800-151938400	Enhancers	Brain Germinal Matrix	brain
2	chr5:151935600-151937800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:151935800-151937600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:151936000-151937600	Enhancers	Fetal Brain Female	brain
5	chr5:151936000-151938200	Enhancers	Fetal Brain Male	brain
6	chr5:151937000-151946200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:151937000-151946800	Weak transcription	Brain Substantia Nigra	brain

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