Variant report

Variant	rs3116457
Chromosome Location	chr8:104282795-104282796
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1138873	0.89[AMR][1000 genomes]
rs12541167	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12543038	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13275377	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13278361	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13278540	0.89[AMR][1000 genomes]
rs1353212	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1353213	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1403293	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494278	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1522707	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1522713	0.81[AMR][1000 genomes]
rs1568641	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16870243	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16870245	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16870249	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17205332	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17799604	0.83[AMR][1000 genomes]
rs1982892	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1982893	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2131860	0.81[AMR][1000 genomes]
rs2220825	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2270525	0.85[AMR][1000 genomes]
rs3104029	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3104031	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3107646	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3107648	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3107649	0.82[AMR][1000 genomes]
rs3116462	0.90[AMR][1000 genomes]
rs3116464	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3116466	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3116468	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3133820	0.88[AMR][1000 genomes]
rs3133821	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3133824	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3133825	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34185273	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34201011	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34273148	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34337822	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3116457	FLJ11184	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104268200-104283400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:104269000-104283400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:104269800-104283200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:104269800-104283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:104279400-104282800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:104279600-104282800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr8:104279600-104282800	Enhancers	NHLF	lung
8	chr8:104280000-104283400	Weak transcription	Aorta	Aorta
9	chr8:104280200-104283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:104280800-104283000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:104281000-104282800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr8:104281800-104283000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:104282000-104282800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:104282000-104283400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:104282000-104283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr8:104282200-104283000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:104282400-104284000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:104282600-104283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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