Variant report

Variant	rs2275788
Chromosome Location	chr20:23338694-23338695
allele	A/G
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	MAX	chr20:23338177-23339261	ECC-1	luminal epithelium:	n/a	chr20:23338835-23338848 chr20:23338836-23338847 chr20:23338837-23338846 chr20:23338837-23338846 chr20:23338859-23338869 chr20:23338835-23338848 chr20:23338837-23338846 chr20:23338836-23338847 chr20:23338836-23338845
2	POLR2A	chr20:23338109-23339344	GM12892	blood:	n/a	n/a
3	NRF1	chr20:23338264-23339468	GM12878	blood:	n/a	chr20:23339002-23339016 chr20:23339066-23339080 chr20:23339068-23339079 chr20:23339069-23339080 chr20:23339057-23339068
4	POLR2A	chr20:23338314-23339374	NB4	blood:	n/a	n/a
5	GTF2F1	chr20:23338588-23339130	K562	blood:	n/a	n/a
6	POLR2A	chr20:23337640-23339345	HUVEC	blood vessel:	n/a	n/a
7	TBP	chr20:23338461-23339279	K562	blood:	n/a	n/a
8	POLR2A	chr20:23338118-23339054	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr20:23338248-23339381	HepG2	liver:	n/a	n/a
10	ATF2	chr20:23338462-23339394	GM12878	blood:	n/a	n/a
11	MAX	chr20:23338270-23339181	K562	blood:	n/a	chr20:23338835-23338848 chr20:23338836-23338847 chr20:23338837-23338846 chr20:23338837-23338846 chr20:23338859-23338869 chr20:23338835-23338848 chr20:23338837-23338846 chr20:23338836-23338847 chr20:23338836-23338845
12	POLR2A	chr20:23338333-23338888	Hela-S3	cervix:	n/a	n/a
13	NFYA	chr20:23338564-23339296	Hela-S3	cervix:	n/a	chr20:23338945-23338955 chr20:23338943-23338958 chr20:23338943-23338957 chr20:23338943-23338958
14	BHLHE40	chr20:23338669-23339182	A549	lung:	n/a	n/a
15	POLR2A	chr20:23338519-23339312	HL-60	blood:	n/a	n/a
16	NRF1	chr20:23338433-23339421	SK-N-SH	brain:	n/a	chr20:23339002-23339016 chr20:23339066-23339080 chr20:23339068-23339079 chr20:23339069-23339080 chr20:23339057-23339068
17	SIN3A	chr20:23338190-23339194	H1-hESC	embryonic stem cell:	n/a	chr20:23338838-23338847 chr20:23338836-23338845
18	TEAD4	chr20:23338582-23338936	K562	blood:	n/a	n/a
19	USF1	chr20:23338421-23339211	A549	lung:	n/a	chr20:23338836-23338847
20	UBTF	chr20:23338386-23338821	K562	blood:	n/a	n/a
21	EBF1	chr20:23338264-23339338	GM12878	blood:	n/a	n/a
22	MAX	chr20:23338469-23339113	HUVEC	blood vessel:	n/a	chr20:23338835-23338848 chr20:23338836-23338847 chr20:23338837-23338846 chr20:23338837-23338846 chr20:23338859-23338869 chr20:23338835-23338848 chr20:23338837-23338846 chr20:23338836-23338847 chr20:23338836-23338845
23	POLR2A	chr20:23338166-23338934	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr20:23337680-23339379	K562	blood:	n/a	n/a
25	HCFC1	chr20:23338510-23339147	K562	blood:	n/a	n/a
26	TAF1	chr20:23338297-23339162	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr20:23338414-23339248	SK-N-SH	brain:	n/a	chr20:23338835-23338848 chr20:23338836-23338847 chr20:23338837-23338846 chr20:23338837-23338846 chr20:23338859-23338869 chr20:23338835-23338848 chr20:23338837-23338846 chr20:23338836-23338847 chr20:23338836-23338845
28	GATA3	chr20:23338434-23338920	T-47D	breast:	n/a	n/a
29	YY1	chr20:23338469-23338861	A549	lung:	n/a	n/a
30	SIN3AK20	chr20:23338426-23338892	A549	lung:	n/a	n/a
31	POLR2A	chr20:23336781-23339672	Hela-S3	cervix:	n/a	n/a
32	ZEB1	chr20:23338483-23339120	GM12878	blood:	n/a	chr20:23339024-23339031
33	TAF1	chr20:23338532-23339165	H1-neurons	neurons:	n/a	n/a
34	NFYA	chr20:23338625-23339073	K562	blood:	n/a	chr20:23338945-23338955 chr20:23338943-23338958 chr20:23338943-23338957 chr20:23338943-23338958
35	MAFF	chr20:23338624-23339025	HepG2	liver:	n/a	n/a
36	CTBP2	chr20:23338424-23339033	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr20:23337428-23339014	GM12892	blood:	n/a	n/a
38	HEY1	chr20:23338339-23339303	HepG2	liver:	n/a	chr20:23338848-23338863
39	CHD2	chr20:23338321-23339176	Hela-S3	cervix:	n/a	n/a
40	SRF	chr20:23338612-23338949	HepG2	liver:	n/a	chr20:23338859-23338869
41	NR2F2	chr20:23338325-23339174	MCF-7	breast:	n/a	n/a
42	TCF12	chr20:23338229-23339371	A549	lung:	n/a	chr20:23338314-23338324
43	ARID3A	chr20:23338289-23338942	K562	blood:	n/a	n/a
44	JUN	chr20:23338296-23339255	K562	blood:	n/a	n/a
45	POLR2A	chr20:23338321-23339156	Gliobla	brain:	n/a	n/a
46	USF2	chr20:23338639-23339011	K562	blood:	n/a	chr20:23338836-23338847
47	MAFK	chr20:23338231-23339161	Hela-S3	cervix:	n/a	n/a
48	FOS	chr20:23338657-23339100	MCF10A-Er-Src	breast:	n/a	n/a
49	RCOR1	chr20:23338417-23339169	K562	blood:	n/a	n/a
50	MXI1	chr20:23338283-23339530	GM12878	blood:	n/a	chr20:23338838-23338847

No.	Distal block	Cell Line	Cell type
1	chr17:79481126..79481770-chr20:23338177..23338960,2	Hela-S3	cervix:
2	chr19:10443979..10444576-chr20:23338067..23338836,2	NB4	blood:
3	chr20:23337918..23344174-chr20:23400107..23404916,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NAPB-1	chr20:23338592-23338753	XLOC_013693
2	lnc-NAPB-1	chr20:23338592-23338851	XLOC_013693
3	lnc-NAPB-1	chr20:23338592-23338808	NONHSAT079053
4	lnc-NAPB-1	chr20:23338592-23338808	NONHSAT079055
5	lnc-NAPB-1	chr20:23338592-23338764	NR_109884

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000232645	TF binding region
ENSG00000269407	TF binding region
ENSG00000184009	Chromatin interaction
ENSG00000161847	Chromatin interaction
ENSG00000125814	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1056394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11087428	0.85[EUR][1000 genomes]
rs11905630	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1419005	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419006	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419009	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419010	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16985308	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1936013	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2000261	0.88[ASN][1000 genomes]
rs2051093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144381	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2224074	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236022	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249943	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2251145	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275787	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281429	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424528	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424530	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424531	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424534	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424535	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424536	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424537	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424539	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424540	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424541	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424544	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424545	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424546	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424548	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424549	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424550	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424551	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424552	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424554	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424556	0.85[EUR][1000 genomes]
rs2424557	0.84[EUR][1000 genomes]
rs3746734	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813490	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813491	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813493	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4813495	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4815199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815203	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048778	0.90[ASN][1000 genomes]
rs6076057	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6076059	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6076071	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6076073	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6083083	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083084	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083085	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083087	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083088	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6083092	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083095	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083099	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6083100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6083104	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083110	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083111	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083119	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6114085	0.85[EUR][1000 genomes]
rs6132604	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132607	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6132612	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137899	0.91[ASN][1000 genomes]
rs6137905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137908	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137909	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137922	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137924	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137934	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137940	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137949	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7269627	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743022	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs743023	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs743024	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761726	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7988	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8118688	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8183442	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2275788	NAPB	Cis_1M	lymphoblastoid	RTeQTL
rs2275788	NAPB	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23336800-23339200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr20:23336800-23339200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr20:23336800-23339200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr20:23336800-23339400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr20:23337600-23338800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr20:23337600-23339200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:23337600-23339200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr20:23337600-23339200	Active TSS	Thymus	Thymus
9	chr20:23337600-23339400	Active TSS	NHLF	lung
10	chr20:23337600-23339600	Active TSS	Stomach Smooth Muscle	stomach
11	chr20:23337800-23339200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr20:23337800-23339400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:23337800-23339600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:23337800-23339800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:23338000-23338800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr20:23338000-23338800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:23338000-23338800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:23338000-23338800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr20:23338000-23338800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr20:23338000-23339000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:23338000-23339200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr20:23338000-23339200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:23338000-23339200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr20:23338000-23339200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr20:23338000-23339200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr20:23338000-23339200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr20:23338000-23339200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr20:23338000-23339200	Active TSS	A549	lung
29	chr20:23338000-23339200	Active TSS	GM12878-XiMat	blood
30	chr20:23338000-23339200	Active TSS	Hela-S3	cervix
31	chr20:23338000-23339200	Active TSS	HSMMtube	muscle
32	chr20:23338000-23339200	Active TSS	K562	blood
33	chr20:23338000-23339200	Active TSS	NHDF-Ad	bronchial
34	chr20:23338000-23339400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:23338000-23339400	Active TSS	Fetal Intestine Large	intestine
36	chr20:23338000-23339400	Active TSS	Fetal Intestine Small	intestine
37	chr20:23338000-23339400	Active TSS	Psoas Muscle	Psoas
38	chr20:23338000-23339600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:23338000-23339600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:23338200-23338800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:23338200-23338800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:23338200-23338800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr20:23338200-23338800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr20:23338200-23338800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr20:23338200-23338800	Active TSS	Stomach Mucosa	stomach
46	chr20:23338200-23339000	Active TSS	NHEK	skin
47	chr20:23338200-23339200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr20:23338200-23339200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr20:23338200-23339200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:23338200-23339200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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