Variant report

Variant	rs12450620
Chromosome Location	chr17:46130254-46130255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr17:46130153-46130271	GM12878	blood:	n/a	n/a
2	MXI1	chr17:46128649-46132036	IMR90	lung:	n/a	n/a
3	POLR2A	chr17:46129079-46130587	K562	blood:	n/a	n/a
4	MXI1	chr17:46128980-46133584	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr17:46130109-46130846	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:46129738-46130491	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr17:46127640-46130485	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:46130188-46130412	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr17:46130085-46130484	HepG2	liver:	n/a	n/a
10	CTCF	chr17:46130160-46130310	HMF	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46129155..46131443-chr17:46151423..46153191,2	K562	blood:
2	chr17:46033378..46035935-chr17:46129952..46132940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263412	TF binding region
NFE2L1	TF binding region
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1010228	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1010230	0.81[ASN][1000 genomes]
rs10853094	0.82[EUR][1000 genomes]
rs11079806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11079808	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11079809	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11649919	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11651097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869625	0.83[AMR][1000 genomes]
rs12600980	0.89[ASN][1000 genomes]
rs12936731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939514	0.80[ASN][1000 genomes]
rs12941295	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12943543	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12946143	0.98[ASN][1000 genomes]
rs12949879	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12950213	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12950402	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12952163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468270	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16951519	0.98[ASN][1000 genomes]
rs1860866	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2051821	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2109983	0.81[ASN][1000 genomes]
rs2109984	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2229369	0.99[ASN][1000 genomes]
rs2240120	0.94[ASN][1000 genomes]
rs2240121	0.98[ASN][1000 genomes]
rs2285863	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2325783	0.98[ASN][1000 genomes]
rs35361214	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35688835	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3744346	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744347	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3785737	0.85[ASN][1000 genomes]
rs4794441	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794448	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794449	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794450	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4794451	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794453	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4995899	0.98[ASN][1000 genomes]
rs55920502	0.98[ASN][1000 genomes]
rs58203448	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58595405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58624511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62064953	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504024	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504025	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504031	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504032	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71369829	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7209585	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7209730	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7212202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213339	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7217496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7218700	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7220520	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7221441	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7222136	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7224014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7224461	0.81[ASN][1000 genomes]
rs741058	0.81[ASN][1000 genomes]
rs8065670	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8065993	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8066049	0.82[ASN][1000 genomes]
rs8066391	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8069889	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8071199	0.87[ASN][1000 genomes]
rs8075500	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8076380	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8077860	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8078125	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8080662	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs875065	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs875066	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9747001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978263	0.89[ASN][1000 genomes]
rs9807087	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9890691	0.89[ASN][1000 genomes]
rs9899275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910516	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12450620	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs12450620	CBX1	Cis_1M	lymphoblastoid	RTeQTL
rs12450620	SNX11	cis	Whole Blood	GTEx
rs12450620	SNX11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46124400-46132200	Active TSS	Psoas Muscle	Psoas
2	chr17:46126800-46131200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:46127400-46131600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:46127600-46131000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:46127600-46131000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr17:46127600-46131800	Genic enhancers	Fetal Stomach	stomach
7	chr17:46127600-46132800	Genic enhancers	Fetal Intestine Small	intestine
8	chr17:46127800-46130600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr17:46127800-46130800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:46127800-46130800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr17:46127800-46131000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr17:46127800-46131200	Transcr. at gene 5' and 3'	HepG2	liver
13	chr17:46127800-46131600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr17:46127800-46132000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:46127800-46132600	Genic enhancers	Fetal Thymus	thymus
16	chr17:46127800-46133000	Genic enhancers	Fetal Intestine Large	intestine
17	chr17:46127800-46133200	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr17:46127800-46133200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr17:46127800-46133200	Genic enhancers	Placenta	Placenta
20	chr17:46127800-46133200	Genic enhancers	Pancreas	Pancrea
21	chr17:46127800-46133400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:46127800-46133600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:46128000-46130400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:46128000-46130400	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr17:46128000-46130400	Genic enhancers	Brain Cingulate Gyrus	brain
26	chr17:46128000-46130400	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
27	chr17:46128000-46130800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr17:46128000-46130800	Genic enhancers	H1 Cell Line	embryonic stem cell
29	chr17:46128000-46130800	Genic enhancers	Fetal Lung	lung
30	chr17:46128000-46131200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr17:46128000-46131200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
32	chr17:46128000-46131600	Genic enhancers	Esophagus	oesophagus
33	chr17:46128000-46131600	Transcr. at gene 5' and 3'	NHEK	skin
34	chr17:46128000-46131800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr17:46128000-46131800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
36	chr17:46128000-46132000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:46128000-46132600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:46128000-46132600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
39	chr17:46128000-46133000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
40	chr17:46128000-46133200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr17:46128000-46133800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:46128000-46134000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:46128000-46134000	Genic enhancers	Gastric	stomach
44	chr17:46128000-46134000	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr17:46128000-46134400	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr17:46128000-46138000	Genic enhancers	Spleen	Spleen
47	chr17:46128200-46130400	Transcr. at gene 5' and 3'	HSMM	muscle
48	chr17:46128200-46130600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr17:46128200-46130600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
50	chr17:46128200-46130800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle

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