Variant report

Variant	rs10489507
Chromosome Location	chr1:84279930-84279931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10157076	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10158343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040576	0.87[ASN][1000 genomes]
rs10430047	0.81[ASN][1000 genomes]
rs10430048	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10430063	0.81[ASN][1000 genomes]
rs10430064	0.81[ASN][1000 genomes]
rs10465742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489506	0.88[ASN][1000 genomes]
rs10782820	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10874420	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10874421	0.81[ASN][1000 genomes]
rs10874422	0.81[ASN][1000 genomes]
rs11163829	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11163832	0.81[ASN][1000 genomes]
rs11163833	0.81[ASN][1000 genomes]
rs11163835	0.81[ASN][1000 genomes]
rs11163837	0.81[ASN][1000 genomes]
rs11163838	0.81[ASN][1000 genomes]
rs11163839	0.81[ASN][1000 genomes]
rs11163840	1.00[JPT][hapmap]
rs11163842	0.81[ASN][1000 genomes]
rs11163847	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163848	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12028642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029461	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033859	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035289	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12041369	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12044606	0.81[ASN][1000 genomes]
rs12045391	0.81[ASN][1000 genomes]
rs12048434	0.85[ASN][1000 genomes]
rs12057556	0.89[ASN][1000 genomes]
rs12059428	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12067203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12069168	0.86[ASN][1000 genomes]
rs12070108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12071975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12074729	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12080974	0.81[ASN][1000 genomes]
rs12082383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12082518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085122	0.81[ASN][1000 genomes]
rs12085367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087099	0.81[ASN][1000 genomes]
rs12088221	0.81[ASN][1000 genomes]
rs12088867	0.81[ASN][1000 genomes]
rs12091588	0.81[ASN][1000 genomes]
rs12092736	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17129275	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17129297	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17129321	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17129344	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17129416	0.81[ASN][1000 genomes]
rs17129475	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17129836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17129848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17129850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17129859	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129909	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1951928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057084	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28476757	0.81[ASN][1000 genomes]
rs35299117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4001468	0.89[ASN][1000 genomes]
rs4140461	0.81[ASN][1000 genomes]
rs55958267	0.88[ASN][1000 genomes]
rs60743554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61766224	0.91[AMR][1000 genomes]
rs61767991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714280	0.81[ASN][1000 genomes]
rs717234	0.81[ASN][1000 genomes]
rs72952444	0.81[ASN][1000 genomes]
rs742779	0.89[ASN][1000 genomes]
rs7529582	0.84[EUR][1000 genomes]
rs969125	0.81[ASN][1000 genomes]
rs969126	0.81[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489507	LPHN2	cis	cerebellum	SCAN
rs10489507	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84273800-84281000	Weak transcription	Adipose Nuclei	Adipose
2	chr1:84276600-84281000	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:84279800-84280000	Enhancers	Right Atrium	heart
4	chr1:84279800-84282800	Enhancers	Liver	Liver

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