Variant report

Variant	rs4958561
Chromosome Location	chr5:151930231-151930232
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	chr5:151928150..151931020-chr5:152818556..152820220,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10036750	0.81[EUR][1000 genomes]
rs10045463	0.81[EUR][1000 genomes]
rs10155517	0.91[AMR][1000 genomes];0.99[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	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13359939	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13361438	0.87[ASN][1000 genomes]
rs17452991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453481	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17453530	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17453740	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17453775	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454420	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17549307	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17549488	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17550343	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17565365	0.95[ASN][1000 genomes]
rs17565693	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2961741	0.82[EUR][1000 genomes]
rs2961756	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961760	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961765	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961766	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964223	0.84[EUR][1000 genomes]
rs2964230	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964231	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923209	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246030	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4246033	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4342320	0.87[AFR][1000 genomes];0.80[EUR][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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484412	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4557395	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4580766	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958316	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958317	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958320	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958323	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958537	1.00[JPT][hapmap]
rs4958551	1.00[AFR][1000 genomes]
rs4958554	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4958555	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4958560	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958562	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4958564	0.90[AMR][1000 genomes];0.84[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	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958569	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55648729	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55696164	1.00[AFR][1000 genomes]
rs55786399	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56014830	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56050684	1.00[AFR][1000 genomes]
rs67979431	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871699	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6876403	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6876723	0.89[AMR][1000 genomes];0.97[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]
rs72795336	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795339	0.80[EUR][1000 genomes]
rs72795340	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795344	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795349	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795350	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795351	0.87[AFR][1000 genomes]
rs72795352	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72795364	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72795366	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72795376	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795389	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72797226	0.95[ASN][1000 genomes]
rs72797233	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797237	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797241	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797243	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797251	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72797254	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797262	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72797296	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[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:2 , 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
2	nsv1028516	chr5:151896509-151930647	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4958561	SLC26A2	cis	cerebellum	SCAN
rs4958561	GALNTL2	trans	cerebellum	SCAN
rs4958561	GLRA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151928200-151936000	Weak transcription	Fetal Brain Male	brain

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