Variant report

Variant	rs4794450
Chromosome Location	chr17:46184093-46184094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46183496-46184633	K562	blood:	n/a	n/a
2	SIN3AK20	chr17:46184051-46186425	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46032611..46035777-chr17:46183682..46186625,3	MCF-7	breast:
2	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
3	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:
4	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
5	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
6	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
7	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
8	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
9	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

No data

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000167183	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000108468	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1010228	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1010230	0.87[ASN][1000 genomes]
rs10853094	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10853097	0.83[ASN][1000 genomes]
rs11079806	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11079807	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11079808	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079809	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11649919	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11651097	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11655407	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11869625	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450620	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12600980	0.94[ASN][1000 genomes]
rs12602948	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12936731	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12939514	0.88[ASN][1000 genomes]
rs12941295	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12943543	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946143	0.86[ASN][1000 genomes]
rs12949879	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12950213	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12950402	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12952163	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1468270	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16951519	0.86[ASN][1000 genomes]
rs1860866	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051821	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208005	0.81[ASN][1000 genomes]
rs208008	0.83[ASN][1000 genomes]
rs208009	0.83[ASN][1000 genomes]
rs208019	0.81[ASN][1000 genomes]
rs2109983	0.87[ASN][1000 genomes]
rs2109984	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2229369	0.85[ASN][1000 genomes]
rs2240120	0.83[ASN][1000 genomes]
rs2240121	0.86[ASN][1000 genomes]
rs2285863	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2325783	0.86[ASN][1000 genomes]
rs2325784	0.82[ASN][1000 genomes]
rs2325804	0.83[ASN][1000 genomes]
rs35361214	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35688835	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744346	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744347	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3785737	0.90[ASN][1000 genomes]
rs3815472	0.83[ASN][1000 genomes]
rs4794441	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794442	0.84[ASN][1000 genomes]
rs4794443	0.80[AFR][1000 genomes]
rs4794448	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794449	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794451	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794453	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4995899	0.86[ASN][1000 genomes]
rs55920502	0.86[ASN][1000 genomes]
rs58203448	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58595405	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58624511	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62064953	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6504024	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6504025	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6504031	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6504032	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71356520	0.85[ASN][1000 genomes]
rs71356521	0.81[ASN][1000 genomes]
rs71369829	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7209585	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7209730	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7212202	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7213339	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217496	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7218700	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7220520	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7221441	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7222136	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7224014	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224461	0.87[ASN][1000 genomes]
rs741058	0.87[ASN][1000 genomes]
rs8065670	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065993	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066049	0.87[ASN][1000 genomes]
rs8066391	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069889	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071199	0.92[ASN][1000 genomes]
rs8075500	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076380	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8077860	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8078125	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8079616	0.83[ASN][1000 genomes]
rs8080662	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875065	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs875066	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9747001	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978263	0.94[ASN][1000 genomes]
rs9807087	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9890691	0.94[ASN][1000 genomes]
rs9899275	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9899461	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9910516	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[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	nsv112217	chr17:46182711-46190093	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4794450	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs4794450	SNX11	cis	Whole Blood	GTEx
rs4794450	SNX11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46178400-46184200	Weak transcription	Fetal Heart	heart
2	chr17:46179200-46184200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr17:46179200-46184200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:46179200-46184200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:46179200-46184200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:46179200-46184200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr17:46179200-46184200	Weak transcription	Left Ventricle	heart
8	chr17:46179200-46184200	Weak transcription	Pancreas	Pancrea
9	chr17:46179200-46184200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:46179200-46184400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:46179400-46184200	Weak transcription	Primary T cells from cord blood	blood
12	chr17:46179400-46184200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr17:46179400-46184200	Weak transcription	Colonic Mucosa	Colon
14	chr17:46179400-46184200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:46179400-46184200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr17:46179600-46184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:46179600-46184200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:46179600-46184200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr17:46179600-46184200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:46179600-46184200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:46179600-46184200	Weak transcription	Colon Smooth Muscle	Colon
24	chr17:46179600-46184200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:46179600-46184200	Weak transcription	NHEK	skin
26	chr17:46179600-46184400	Weak transcription	NHDF-Ad	bronchial
27	chr17:46179800-46184400	Weak transcription	Small Intestine	intestine
28	chr17:46181000-46184200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr17:46181000-46184200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr17:46181200-46184200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr17:46181200-46184200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr17:46182400-46184200	Weak transcription	Fetal Brain Male	brain
33	chr17:46182600-46184400	Enhancers	Primary B cells from cord blood	blood
34	chr17:46183200-46184400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:46183400-46184200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr17:46183600-46184200	Enhancers	Primary B cells from peripheral blood	blood
37	chr17:46183600-46184200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr17:46183600-46184200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr17:46183600-46184400	Enhancers	Primary hematopoietic stem cells	blood
40	chr17:46183800-46184200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr17:46183800-46184200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:46183800-46184200	Enhancers	Brain Hippocampus Middle	brain
43	chr17:46183800-46184200	Enhancers	GM12878-XiMat	blood
44	chr17:46183800-46184600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr17:46183800-46184800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr17:46184000-46184200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr17:46184000-46184200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr17:46184000-46184200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr17:46184000-46184200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr17:46184000-46184200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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