Variant report

Variant	rs1404365
Chromosome Location	chr8:85899272-85899273
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10046686	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10081441	0.94[ASN][1000 genomes]
rs10088120	0.90[JPT][hapmap]
rs10088722	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10091232	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10091245	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10094238	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10094828	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10095636	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10095682	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10099017	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100687	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10100806	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10104630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10104687	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10105658	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10109018	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10110570	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10110879	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1025232	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958229	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958230	0.94[ASN][1000 genomes]
rs10958232	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958233	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11261468	0.82[JPT][hapmap]
rs11775584	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12542468	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12675186	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13267859	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs13273360	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1365668	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1365677	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1365678	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1524642	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17811680	0.91[ASN][1000 genomes]
rs1851973	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1946400	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991347	0.97[ASN][1000 genomes]
rs1991348	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991349	0.97[ASN][1000 genomes]
rs1991350	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991351	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991352	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059678	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059679	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059680	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081673	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140688	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403088	0.82[JPT][hapmap]
rs2712	0.97[ASN][1000 genomes]
rs28592585	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896454	0.90[JPT][hapmap]
rs34103685	0.90[JPT][hapmap]
rs34327710	0.84[ASN][1000 genomes]
rs35068782	0.91[ASN][1000 genomes]
rs35382421	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779899	0.90[JPT][hapmap]
rs3900098	0.97[ASN][1000 genomes]
rs3937521	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3942601	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740035	0.91[ASN][1000 genomes]
rs6605624	0.81[JPT][hapmap]
rs6990756	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7003643	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008839	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7010343	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015758	0.91[JPT][hapmap]
rs7829050	0.91[JPT][hapmap]
rs7829144	0.82[JPT][hapmap]
rs7832097	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7838564	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7838940	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7841142	0.82[JPT][hapmap]
rs9298433	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9650296	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965734	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9692810	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9692962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9693371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987477	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv427823	chr8:85538522-86009068	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv428203	chr8:85834033-86009068	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1404365	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs1404365	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs1404365	LRRCC1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:85897200-85900800	Weak transcription	HMEC	breast

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