Variant report

Variant	rs8069889
Chromosome Location	chr17:46192282-46192283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1010228	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1010230	0.81[ASN][1000 genomes]
rs10853094	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079806	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11079807	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11079808	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079809	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11649919	0.83[EUR][1000 genomes]
rs11651097	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11655407	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11869625	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12450620	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12600980	0.88[ASN][1000 genomes]
rs12602948	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12936731	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12941295	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12943543	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12949879	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12950213	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12950402	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12952163	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1452665	0.81[AMR][1000 genomes]
rs1860866	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2051821	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2109983	0.81[ASN][1000 genomes]
rs2109984	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2285863	0.81[AMR][1000 genomes]
rs2325885	0.82[AMR][1000 genomes]
rs35361214	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35688835	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3744346	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744347	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3785737	0.84[ASN][1000 genomes]
rs4794441	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794442	0.88[ASN][1000 genomes]
rs4794448	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794449	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794450	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4794451	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794453	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58203448	0.84[AMR][1000 genomes]
rs58595405	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58624511	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62064953	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6504024	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6504025	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6504031	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504032	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6847	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71369829	0.85[EUR][1000 genomes]
rs7209585	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7209730	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7212202	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7213339	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7217496	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7218700	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7220520	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7221441	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222136	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7224014	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7224461	0.81[ASN][1000 genomes]
rs741058	0.81[ASN][1000 genomes]
rs8065670	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8065993	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066049	0.87[ASN][1000 genomes]
rs8066391	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8071199	0.86[ASN][1000 genomes]
rs8075500	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8076380	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077860	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8078125	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8080662	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs875065	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs875066	0.81[EUR][1000 genomes]
rs9747001	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs978263	0.88[ASN][1000 genomes]
rs9807087	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9890691	0.88[ASN][1000 genomes]
rs9899275	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9899461	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9903692	0.82[AMR][1000 genomes]
rs9909933	0.82[AMR][1000 genomes]
rs9910516	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv1007058	chr17:46188741-46200367	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8069889	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs8069889	SNX11	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46185800-46193000	Weak transcription	Gastric	stomach
2	chr17:46185800-46195800	Weak transcription	Ovary	ovary
3	chr17:46186000-46195200	Weak transcription	Aorta	Aorta
4	chr17:46186000-46196200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr17:46186000-46198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46186200-46192600	Weak transcription	Colon Smooth Muscle	Colon
7	chr17:46186200-46192600	Weak transcription	A549	lung
8	chr17:46186200-46193800	Weak transcription	Fetal Lung	lung
9	chr17:46186200-46195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:46186200-46195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:46186200-46196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:46186200-46198600	Weak transcription	Fetal Brain Male	brain
13	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:46186400-46192400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:46186400-46193000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:46186400-46193000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr17:46186400-46193400	Weak transcription	Osteobl	bone
18	chr17:46186400-46193600	Weak transcription	HSMMtube	muscle
19	chr17:46186400-46194800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:46186400-46195000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr17:46186400-46195000	Weak transcription	HSMM	muscle
22	chr17:46186400-46195000	Weak transcription	NHDF-Ad	bronchial
23	chr17:46186400-46195200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:46186400-46195400	Weak transcription	Brain Angular Gyrus	brain
25	chr17:46186400-46195400	Weak transcription	NH-A	brain
26	chr17:46186400-46196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:46186400-46196000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:46186400-46198600	Weak transcription	Small Intestine	intestine
29	chr17:46186400-46198800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr17:46186600-46192600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:46186600-46195000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:46186600-46195200	Weak transcription	Stomach Mucosa	stomach
33	chr17:46186600-46196000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr17:46187600-46198400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr17:46188000-46192400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:46188000-46192400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:46188200-46192600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr17:46188200-46195000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:46188200-46201200	Strong transcription	Fetal Intestine Small	intestine
40	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr17:46188400-46195000	Weak transcription	Brain Substantia Nigra	brain
42	chr17:46188400-46201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:46188600-46194800	Weak transcription	HUVEC	blood vessel
44	chr17:46188600-46195000	Weak transcription	Pancreas	Pancrea
45	chr17:46188600-46196200	Weak transcription	Psoas Muscle	Psoas
46	chr17:46188800-46192400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr17:46189000-46202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:46189200-46197800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:46189200-46199000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:46189400-46198600	Strong transcription	Brain Anterior Caudate	brain

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