Variant report

Variant	rs9747001
Chromosome Location	chr17:46154669-46154670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46124283..46126892-chr17:46151852..46155065,3	K562	blood:
2	chr17:46143868..46147268-chr17:46149730..46155245,6	K562	blood:

Variant related genes	Relation type
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1010228	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1010230	0.82[ASN][1000 genomes]
rs10853094	0.84[EUR][1000 genomes]
rs11079806	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11079808	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11079809	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11649919	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11869625	0.83[AMR][1000 genomes]
rs12450620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600980	0.90[ASN][1000 genomes]
rs12936731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939514	0.81[ASN][1000 genomes]
rs12941295	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12943543	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12946143	0.99[ASN][1000 genomes]
rs12949879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12950213	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12950402	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12952163	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468270	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16951519	0.99[ASN][1000 genomes]
rs1860866	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051821	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109983	0.82[ASN][1000 genomes]
rs2109984	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2229369	0.98[ASN][1000 genomes]
rs2240120	0.96[ASN][1000 genomes]
rs2240121	0.99[ASN][1000 genomes]
rs2285863	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2325783	0.99[ASN][1000 genomes]
rs35361214	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35688835	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744346	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3744347	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785737	0.86[ASN][1000 genomes]
rs4794441	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794448	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794449	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794450	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794451	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794453	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4995899	0.99[ASN][1000 genomes]
rs55920502	0.99[ASN][1000 genomes]
rs58203448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58595405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58624511	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62064953	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504024	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504025	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504031	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504032	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71356520	0.80[ASN][1000 genomes]
rs71369829	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7209585	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209730	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7212202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7213339	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7217496	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7218700	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7220520	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7221441	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7222136	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7224014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7224461	0.82[ASN][1000 genomes]
rs741058	0.82[ASN][1000 genomes]
rs8065670	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8065993	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066049	0.83[ASN][1000 genomes]
rs8066391	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8069889	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8071199	0.88[ASN][1000 genomes]
rs8075500	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8076380	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8077860	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080662	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875065	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs875066	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978263	0.90[ASN][1000 genomes]
rs9807087	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9890691	0.90[ASN][1000 genomes]
rs9899275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9899461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9903692	0.80[EUR][1000 genomes]
rs9909933	0.80[EUR][1000 genomes]
rs9910516	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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	esv1804681	chr17:46144628-46168544	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9747001	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs9747001	SNX11	cis	Skin Sun Exposed Lower leg	GTEx
rs9747001	SNX11	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46132600-46155200	Strong transcription	Fetal Thymus	thymus
2	chr17:46133000-46155200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:46133200-46157200	Strong transcription	Fetal Stomach	stomach
4	chr17:46133400-46155200	Strong transcription	Dnd41	blood
5	chr17:46135400-46155400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:46137400-46155200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr17:46139200-46162600	Weak transcription	Small Intestine	intestine
8	chr17:46139800-46162600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:46139800-46163600	Weak transcription	Esophagus	oesophagus
10	chr17:46140000-46162400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:46140200-46156400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46140800-46163200	Weak transcription	Colonic Mucosa	Colon
13	chr17:46142600-46162600	Weak transcription	Fetal Heart	heart
14	chr17:46143600-46157400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46143800-46163200	Weak transcription	Aorta	Aorta
16	chr17:46144200-46157000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:46144400-46163000	Weak transcription	Psoas Muscle	Psoas
18	chr17:46144800-46177800	Weak transcription	Right Ventricle	heart
19	chr17:46145800-46155200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:46146400-46158000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:46147800-46177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:46148600-46156600	Strong transcription	Fetal Intestine Small	intestine
23	chr17:46149000-46178000	Weak transcription	Lung	lung
24	chr17:46149200-46162600	Weak transcription	Hela-S3	cervix
25	chr17:46151800-46154800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr17:46151800-46155200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:46151800-46157000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:46152400-46168200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:46152400-46177200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:46152600-46176800	Weak transcription	K562	blood
31	chr17:46152600-46177000	Weak transcription	HSMMtube	muscle
32	chr17:46153400-46170800	Weak transcription	HSMM	muscle
33	chr17:46153800-46162600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr17:46153800-46162600	Weak transcription	Fetal Brain Male	brain
35	chr17:46153800-46176800	Weak transcription	NHLF	lung
36	chr17:46154000-46162200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:46154000-46162400	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:46154000-46163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:46154000-46163200	Weak transcription	Pancreas	Pancrea
40	chr17:46154200-46162400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr17:46154200-46163000	Weak transcription	Adipose Nuclei	Adipose
42	chr17:46154200-46163000	Weak transcription	Brain Substantia Nigra	brain
43	chr17:46154200-46163200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr17:46154200-46163600	Weak transcription	NHDF-Ad	bronchial
45	chr17:46154200-46176800	Weak transcription	HMEC	breast
46	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr17:46154400-46154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:46154400-46158000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:46154400-46162200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr17:46154400-46162200	Weak transcription	Fetal Kidney	kidney

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