Variant report

Variant	rs999466
Chromosome Location	chr8:86395644-86395645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10088136	0.92[ASN][1000 genomes]
rs10095352	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10111039	0.84[ASN][1000 genomes]
rs10504812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504813	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10907474	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11261471	0.82[JPT][hapmap]
rs11261474	0.95[JPT][hapmap]
rs11780285	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985733	0.95[JPT][hapmap]
rs12541445	0.82[JPT][hapmap]
rs12544332	0.86[JPT][hapmap]
rs1303806	0.91[JPT][hapmap]
rs13252971	0.95[JPT][hapmap]
rs13255540	0.80[ASN][1000 genomes]
rs1389245	0.81[ASN][1000 genomes]
rs1389247	0.81[ASN][1000 genomes]
rs1390711	0.91[JPT][hapmap]
rs1493302	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1496526	0.80[EUR][1000 genomes]
rs1496529	0.95[JPT][hapmap]
rs1496530	0.95[JPT][hapmap]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1532423	1.00[JPT][hapmap]
rs1532424	0.95[JPT][hapmap]
rs1553015	0.91[JPT][hapmap]
rs168600	0.80[ASN][1000 genomes]
rs17042	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1845253	0.98[ASN][1000 genomes]
rs1995056	0.86[JPT][hapmap]
rs1995057	0.82[JPT][hapmap]
rs1995058	0.91[JPT][hapmap]
rs2055077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs20571	0.95[JPT][hapmap]
rs2072696	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs2279701	0.82[JPT][hapmap]
rs2291787	0.82[JPT][hapmap]
rs2307075	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2403104	0.91[JPT][hapmap]
rs2403105	0.80[ASN][1000 genomes]
rs2548281	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2645047	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645049	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2645053	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3087782	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs359534	0.80[ASN][1000 genomes]
rs359535	0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs3758076	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3758077	0.81[ASN][1000 genomes]
rs3758078	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs3808539	0.91[JPT][hapmap]
rs4566	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4740049	0.91[JPT][hapmap]
rs4740053	0.91[CHD][hapmap]
rs55641432	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55929157	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58958691	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66498753	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67824746	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6988475	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6997458	1.00[JPT][hapmap]
rs7001359	0.82[JPT][hapmap]
rs7011926	0.91[JPT][hapmap]
rs7016369	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs703	0.95[ASN][1000 genomes]
rs713488	0.81[ASN][1000 genomes]
rs713489	0.81[ASN][1000 genomes]
rs725605	0.90[JPT][hapmap]
rs7386162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903895	0.91[JPT][hapmap]
rs903896	0.91[JPT][hapmap]
rs903897	0.91[JPT][hapmap]
rs9286249	0.84[ASN][1000 genomes]
rs931505	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9329911	0.91[ASN][1000 genomes]
rs955007	0.81[ASN][1000 genomes]
rs9969643	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9987281	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022463	chr8:86257031-86547831	Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1804888	chr8:86263098-86986703	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv831377	chr8:86263107-86444141	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1028148	chr8:86310570-86553130	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv2761206	chr8:86310582-86468868	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs999466	C8orf59	cis	parietal	SCAN
rs999466	C8orf59	cis	cerebellum	SCAN
rs999466	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86377600-86399000	Weak transcription	Fetal Heart	heart
2	chr8:86378000-86403000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:86387200-86403600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:86389600-86402400	Weak transcription	Pancreas	Pancrea
5	chr8:86390400-86403400	Weak transcription	Stomach Mucosa	stomach
6	chr8:86391400-86396000	Weak transcription	Fetal Intestine Small	intestine
7	chr8:86391400-86396400	Weak transcription	Adipose Nuclei	Adipose
8	chr8:86391800-86396000	Weak transcription	NHEK	skin
9	chr8:86393200-86396200	Weak transcription	Gastric	stomach
10	chr8:86393200-86396600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:86393200-86396600	Weak transcription	Colonic Mucosa	Colon
12	chr8:86393200-86398400	Weak transcription	Lung	lung
13	chr8:86393200-86399200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr8:86393200-86403400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:86393200-86405400	Weak transcription	Fetal Stomach	stomach
16	chr8:86393400-86395800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:86393400-86395800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr8:86393400-86399600	Weak transcription	Psoas Muscle	Psoas
19	chr8:86393400-86403800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:86393400-86403800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr8:86393400-86406800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:86393600-86402600	Weak transcription	Fetal Kidney	kidney
23	chr8:86395000-86395800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
24	chr8:86395000-86396000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:86395000-86396200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:86395000-86396400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr8:86395000-86396400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr8:86395000-86397400	Strong transcription	Brain Hippocampus Middle	brain
29	chr8:86395000-86397400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr8:86395000-86397400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr8:86395000-86398200	Strong transcription	Liver	Liver
32	chr8:86395200-86395800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:86395200-86396000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr8:86395200-86396200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr8:86395200-86396200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr8:86395200-86397200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr8:86395200-86397600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr8:86395400-86395800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr8:86395400-86396200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr8:86395400-86396200	ZNF genes & repeats	Brain Angular Gyrus	brain
41	chr8:86395400-86396200	ZNF genes & repeats	Brain Anterior Caudate	brain
42	chr8:86395400-86396400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:86395400-86396400	ZNF genes & repeats	Brain Substantia Nigra	brain
44	chr8:86395400-86396600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr8:86395400-86396600	Strong transcription	Fetal Lung	lung
46	chr8:86395400-86397400	Strong transcription	Left Ventricle	heart
47	chr8:86395400-86397800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:86395600-86396000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr8:86395600-86396200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
50	chr8:86395600-86396400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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