Variant report

Variant	rs2403089
Chromosome Location	chr8:86063523-86063524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10088120	0.82[EUR][1000 genomes]
rs10091577	0.83[EUR][1000 genomes]
rs10091710	0.84[EUR][1000 genomes]
rs10100442	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11261468	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13249364	0.83[EUR][1000 genomes]
rs13269031	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2278459	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2403082	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403087	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2403088	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896452	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2896453	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2896454	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3779899	0.84[EUR][1000 genomes]
rs3808538	0.86[AMR][1000 genomes]
rs4150862	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150865	0.85[EUR][1000 genomes]
rs4150867	0.84[EUR][1000 genomes]
rs4150868	0.84[EUR][1000 genomes]
rs4150869	0.84[EUR][1000 genomes]
rs4150884	0.84[EUR][1000 genomes]
rs4150942	0.81[ASN][1000 genomes]
rs4740043	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62527168	0.84[EUR][1000 genomes]
rs62527173	0.84[EUR][1000 genomes]
rs6605609	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6605624	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6605625	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67573812	0.86[AMR][1000 genomes]
rs6986704	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990256	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6990449	0.85[AMR][1000 genomes]
rs6990452	0.85[AMR][1000 genomes]
rs7004765	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7007304	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7015758	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72682904	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7814435	0.87[ASN][1000 genomes]
rs7818090	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7823218	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7829050	0.82[EUR][1000 genomes]
rs7829144	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7838900	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7841142	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842013	0.84[EUR][1000 genomes]

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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2403089	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2403089	LRRCC1	cis	Esophagus Mucosa	GTEx
rs2403089	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
2	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr8:86049400-86065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:86062800-86064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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