Variant report

Variant	rs1902234
Chromosome Location	chr8:63890717-63890718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-32K4.2.1-6	chr8:63890420-63897460	NONHSAT126909

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10504360	0.95[ASN][1000 genomes]
rs10504361	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11545078	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11985884	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11989852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11990678	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11992253	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11993022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11994355	0.84[AFR][1000 genomes]
rs16930045	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930047	0.81[AFR][1000 genomes]
rs16930051	0.81[AFR][1000 genomes]
rs16930060	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930066	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930072	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17192653	0.95[ASN][1000 genomes]
rs17194931	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17279320	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17279355	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17279558	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902232	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902233	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902235	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168316	0.81[AFR][1000 genomes]
rs2168317	0.84[AFR][1000 genomes]
rs2353363	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2353364	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2353365	0.85[AFR][1000 genomes]
rs2883147	0.85[AFR][1000 genomes]
rs2883148	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780127	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780129	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4395892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410897	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419801	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4739034	0.84[AFR][1000 genomes]
rs55800505	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56034470	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213868	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339102	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57069084	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57776226	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58554293	0.82[ASN][1000 genomes]
rs58942648	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59169978	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60751452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60889737	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60897253	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61326296	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61518338	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61629446	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508088	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508107	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508108	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508118	0.81[AFR][1000 genomes]
rs62508123	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508154	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508155	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508156	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508157	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508158	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510060	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510061	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510062	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510063	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62510064	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472063	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs66790008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6983643	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983864	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983896	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997520	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015120	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7015302	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72656550	0.95[ASN][1000 genomes]
rs72658344	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72658396	0.95[ASN][1000 genomes]
rs72658400	0.95[ASN][1000 genomes]
rs72659813	0.93[ASN][1000 genomes]
rs7834301	0.90[AFR][1000 genomes];0.98[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	nsv1018879	chr8:63281724-63937632	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1033527	chr8:63673915-64073735	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv890964	chr8:63848556-63898146	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1902234	GGH	cis	Artery Tibial	GTEx
rs1902234	GGH	cis	Nerve Tibial	GTEx
rs1902234	GGH	cis	Skin Sun Exposed Lower leg	GTEx
rs1902234	GGH	cis	Adipose Subcutaneous	GTEx
rs1902234	GGH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63868600-63895800	Weak transcription	Fetal Brain Female	brain
2	chr8:63878000-63892000	Weak transcription	Brain Germinal Matrix	brain

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