Variant report

Variant	rs3826047
Chromosome Location	chr15:73925906-73925907
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	RCOR1	chr15:73925592-73926010	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:73925414-73926217	A549	lung:	n/a	n/a
3	POLR2A	chr15:73925381-73926262	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr15:73925796-73926066	GM12892	blood:	n/a	n/a
5	SP1	chr15:73925678-73926110	GM12878	blood:	n/a	chr15:73925834-73925843 chr15:73925833-73925843 chr15:73925833-73925842 chr15:73925832-73925844 chr15:73925833-73925843 chr15:73925832-73925844 chr15:73925910-73925921 chr15:73925833-73925842
6	MTA3	chr15:73925676-73926268	GM12878	blood:	n/a	n/a
7	TEAD4	chr15:73925595-73926180	K562	blood:	n/a	n/a
8	MXI1	chr15:73925728-73926141	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr15:73925310-73926331	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:73925433-73926279	GM12892	blood:	n/a	n/a
11	POLR2A	chr15:73925231-73926243	GM12892	blood:	n/a	n/a
12	USF1	chr15:73925616-73926305	H1-hESC	embryonic stem cell:	n/a	chr15:73925872-73925885 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925896-73925907 chr15:73925873-73925882 chr15:73925875-73925884 chr15:73925872-73925883
13	ZNF143	chr15:73925636-73926071	H1-hESC	embryonic stem cell:	n/a	chr15:73926029-73926048
14	USF2	chr15:73925692-73926163	HepG2	liver:	n/a	chr15:73925872-73925885 chr15:73925872-73925883 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925896-73925907 chr15:73925873-73925882 chr15:73925875-73925884
15	TAF1	chr15:73925442-73926133	H1-hESC	embryonic stem cell:	n/a	n/a
16	USF1	chr15:73925603-73926355	ECC-1	luminal epithelium:	n/a	chr15:73925872-73925885 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925896-73925907 chr15:73925873-73925882 chr15:73925875-73925884 chr15:73925872-73925883
17	ATF3	chr15:73925699-73926142	GM12878	blood:	n/a	chr15:73925874-73925894
18	ELF1	chr15:73925370-73926049	K562	blood:	n/a	chr15:73925707-73925719 chr15:73925997-73926008 chr15:73925833-73925845
19	POLR2A	chr15:73925407-73926618	K562	blood:	n/a	n/a
20	ZKSCAN1	chr15:73925539-73926928	Hela-S3	cervix:	n/a	n/a
21	WRNIP1	chr15:73925769-73926589	GM12878	blood:	n/a	n/a
22	YY1	chr15:73925647-73926039	HCT-116	colon:	n/a	n/a
23	BHLHE40	chr15:73925515-73926447	K562	blood:	n/a	chr15:73925872-73925885 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925873-73925882 chr15:73925875-73925884
24	MYC	chr15:73925720-73926094	MCF10A-Er-Src	breast:	n/a	chr15:73925873-73925884 chr15:73925874-73925883
25	TBP	chr15:73925641-73927025	Hela-S3	cervix:	n/a	n/a
26	PML	chr15:73925815-73926073	GM12878	blood:	n/a	n/a
27	CEBPD	chr15:73925803-73926212	HepG2	liver:	n/a	n/a
28	TAF1	chr15:73925432-73926223	Hela-S3	cervix:	n/a	n/a
29	MAX	chr15:73925474-73926203	ECC-1	luminal epithelium:	n/a	chr15:73925873-73925884 chr15:73925874-73925883
30	BCL3	chr15:73925741-73926934	A549	lung:	n/a	n/a
31	CBX3	chr15:73925606-73926274	K562	blood:	n/a	n/a
32	MAX	chr15:73925645-73926209	HepG2	liver:	n/a	chr15:73925873-73925884 chr15:73925874-73925883
33	POLR2A	chr15:73925750-73926188	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:73925484-73926222	GM12892	blood:	n/a	n/a
35	ZBTB33	chr15:73925551-73926018	HepG2	liver:	n/a	chr15:73925776-73925791 chr15:73925725-73925735 chr15:73925728-73925738
36	USF1	chr15:73925492-73926232	SK-N-SH	brain:	n/a	chr15:73925872-73925885 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925896-73925907 chr15:73925873-73925882 chr15:73925875-73925884 chr15:73925872-73925883
37	FOS	chr15:73925793-73926047	MCF10A-Er-Src	breast:	n/a	chr15:73925850-73925859 chr15:73925813-73925822
38	USF2	chr15:73925661-73926494	H1-hESC	embryonic stem cell:	n/a	chr15:73925872-73925885 chr15:73925872-73925883 chr15:73925874-73925883 chr15:73925874-73925883 chr15:73925868-73925889 chr15:73925896-73925907 chr15:73925873-73925882 chr15:73925875-73925884
39	MAX	chr15:73925442-73926168	MCF-7	breast:	n/a	chr15:73925873-73925884 chr15:73925874-73925883
40	POLR2A	chr15:73922421-73927147	MCF10A-Er-Src	breast:	n/a	n/a
41	BRCA1	chr15:73925496-73927076	Hela-S3	cervix:	n/a	chr15:73925727-73925736 chr15:73925781-73925790
42	YY1	chr15:73925829-73926009	K562	blood:	n/a	n/a
43	NFYB	chr15:73925617-73926120	K562	blood:	n/a	chr15:73925850-73925865 chr15:73925852-73925864
44	POLR2A	chr15:73925478-73926273	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr15:73925436-73926322	GM12892	blood:	n/a	n/a
46	TAF1	chr15:73925334-73926222	H1-neurons	neurons:	n/a	n/a
47	RCOR1	chr15:73925533-73926172	HepG2	liver:	n/a	n/a
48	ATF3	chr15:73925784-73925969	GM12878	blood:	n/a	chr15:73925874-73925894
49	TBP	chr15:73925405-73926409	H1-hESC	embryonic stem cell:	n/a	n/a
50	SP4	chr15:73925605-73926066	H1-hESC	embryonic stem cell:	n/a	chr15:73925830-73925846 chr15:73925910-73925921

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:73925889-73925939	NB4	blood:	n/a
2	chr15:73925889-73925939	IMR90	lung:	fetal
3	chr15:73925889-73925939	H1-hESC	embryonic stem cell:	embryo
4	chr15:73925889-73925939	PFSK-1	brain:	n/a
5	chr15:73925889-73925939	HPAEpiC	pulmonary alveolar:	n/a
6	chr15:73925889-73925939	HCM	heart:	n/a
7	chr15:73925889-73925939	AG09319	gingival:	n/a
8	chr15:73925889-73925939	HRPEpiC	eye:	n/a
9	chr15:73925889-73925939	A549	lung:	n/a
10	chr15:73925889-73925939	MCF-7	breast:	n/a
11	chr15:73925889-73925939	HUVEC	blood vessel:	n/a
12	chr15:73925889-73925939	HepG2	liver:	n/a
13	chr15:73925889-73925939	HRE	kidney:	n/a
14	chr15:73925889-73925939	ovcar-3	ovarian:	n/a
15	chr15:73925889-73925939	RPTEC	kidney:	n/a
16	chr15:73925889-73925939	PrEC	prostate:	n/a
17	chr15:73925889-73925939	HEK293	kidney:	embryo
18	chr15:73925889-73925939	PANC-1	pancreas:	n/a
19	chr15:73925889-73925939	SKMC	muscle:	n/a
20	chr15:73925889-73925939	K562	blood:	n/a
21	chr15:73925889-73925939	AoSMC	blood vessel:	n/a
22	chr15:73925889-73925939	GM12891	blood:	n/a
23	chr15:73925889-73925939	Hepatocyte	liver:	n/a
24	chr15:73925889-73925939	NT2-D1	testis:	n/a
25	chr15:73925889-73925939	ECC-1	luminal epithelium:	n/a
26	chr15:73925889-73925939	CMK	blood:	n/a
27	chr15:73925889-73925939	SK-N-MC	brain:	n/a
28	chr15:73925889-73925939	HAEpiC	amniotic membrane:	n/a
29	chr15:73925889-73925939	Jurkat	blood:	n/a
30	chr15:73925889-73925939	SAEC	small airway:	n/a
31	chr15:73925889-73925939	GM19239	blood:	n/a
32	chr15:73925889-73925939	MCF10A-Er-Src	breast:	n/a
33	chr15:73925889-73925939	HIPEpiC	eye:	n/a
34	chr15:73925889-73925939	NHBE	bronchial:	n/a
35	chr15:73925889-73925939	SK-N-SH_RA	brain:	n/a
36	chr15:73925889-73925939	HRCEpiC	kidney:	n/a
37	chr15:73925889-73925939	HL-60	blood:	n/a
38	chr15:73925889-73925939	LNCaP	prostate:	n/a
39	chr15:73925889-73925939	BE2_C	brain:	n/a
40	chr15:73925889-73925939	HCF	heart:	n/a
41	chr15:73925889-73925939	U87	brain:	n/a
42	chr15:73925889-73925939	HCT-116	colon:	n/a
43	chr15:73925889-73925939	Hela-S3	cervix:	n/a
44	chr15:73925889-73925939	HEEpiC	esophagus:	n/a
45	chr15:73925889-73925939	NHDF-neo	bronchial:	n/a
46	chr15:73925889-73925939	BJ	skin:	n/a
47	chr15:73925889-73925939	AG04449	skin:	fetal
48	chr15:73925889-73925939	AG04450	lung:	fetal
49	chr15:73925889-73925939	T-47D	breast:	n/a
50	chr15:73925889-73925939	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:73659851..73663146-chr15:73925069..73927598,3	MCF-7	breast:
2	chr15:73925842..73926561-chr18:12991102..12991902,2	Hela-S3	cervix:
3	chr15:73925288..73927166-chr15:74001061..74002856,2	MCF-7	breast:
4	chr15:73925194..73925924-chr6:33589142..33589802,2	Hela-S3	cervix:
5	chr15:73925667..73926363-chr4:26322580..26323106,2	Hela-S3	cervix:
6	chr15:73921937..73932817-chr15:73973872..73983627,19	MCF-7	breast:
7	chr1:179851199..179852167-chr15:73925572..73926175,2	Hela-S3	cervix:
8	chr15:73855450..73858620-chr15:73925363..73927455,3	K562	blood:
9	chr15:73923669..73926089-chr15:78010481..78013463,2	K562	blood:
10	chr15:73925808..73926561-chr5:138089020..138089835,2	Hela-S3	cervix:
11	chr15:73925560..73926224-chr5:10353713..10354237,2	Hela-S3	cervix:
12	chr15:73925349..73926145-chr16:87425650..87426573,2	Hela-S3	cervix:
13	chr15:73925518..73926026-chr5:36606661..36607602,2	Hela-S3	cervix:
14	chr15:73923335..73928580-chr15:73974636..73980559,10	MCF-7	breast:
15	chr15:73925706..73926574-chr16:67280563..67281297,2	Hela-S3	cervix:
16	chr15:73925747..73926314-chr16:31128661..31129435,2	Hela-S3	cervix:
17	chr15:73925071..73926054-chr15:80189041..80189911,2	Hela-S3	cervix:

Variant related genes	Relation type
NPTN	TF binding region
NPTN	CpG island
ENSG00000079215	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000135740	Chromatin interaction
ENSG00000259802	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000044115	Chromatin interaction
ENSG00000169783	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000168214	Chromatin interaction
ENSG00000136371	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000103855	Chromatin interaction
ENSG00000140941	Chromatin interaction
ENSG00000156642	Chromatin interaction
ENSG00000145495	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000138622	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11854138	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1585944	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415150	0.81[EUR][1000 genomes]
rs2415151	0.81[EUR][1000 genomes]
rs3825859	0.82[JPT][hapmap]
rs8031286	0.89[EUR][1000 genomes]
rs8032265	0.86[EUR][1000 genomes]
rs8039395	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73922400-73926000	Active TSS	Stomach Smooth Muscle	stomach
2	chr15:73922600-73926000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr15:73922800-73926000	Active TSS	Fetal Intestine Small	intestine
4	chr15:73922800-73926200	Active TSS	Right Atrium	heart
5	chr15:73922800-73926400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:73923000-73926000	Active TSS	Fetal Intestine Large	intestine
7	chr15:73923200-73926000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:73923200-73926000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:73923200-73926000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:73923200-73926000	Active TSS	Right Ventricle	heart
11	chr15:73923400-73926000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:73923400-73926000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:73923400-73926200	Active TSS	Aorta	Aorta
14	chr15:73923400-73926200	Active TSS	Left Ventricle	heart
15	chr15:73923600-73926000	Active TSS	Colon Smooth Muscle	Colon
16	chr15:73923600-73926400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr15:73923800-73926000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr15:73923800-73926000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:73923800-73926000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:73923800-73926000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:73923800-73926000	Active TSS	Rectal Smooth Muscle	rectum
22	chr15:73923800-73926000	Active TSS	NHDF-Ad	bronchial
23	chr15:73923800-73926000	Active TSS	NHLF	lung
24	chr15:73923800-73926200	Active TSS	GM12878-XiMat	blood
25	chr15:73924000-73926000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:73924000-73926000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:73924000-73926000	Active TSS	HSMM	muscle
28	chr15:73924200-73926000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:73924200-73926000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr15:73924200-73926000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:73924200-73926200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:73924200-73926200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:73924200-73926200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:73924200-73926200	Active TSS	Esophagus	oesophagus
35	chr15:73924200-73926200	Active TSS	Fetal Muscle Trunk	muscle
36	chr15:73924200-73926200	Active TSS	Gastric	stomach
37	chr15:73924200-73926400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr15:73924200-73926400	Active TSS	Lung	lung
39	chr15:73924400-73926000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:73924400-73926000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:73924400-73926000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr15:73924400-73926000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:73924400-73926000	Active TSS	Fetal Stomach	stomach
44	chr15:73924400-73926000	Active TSS	Pancreas	Pancrea
45	chr15:73924400-73926000	Active TSS	A549	lung
46	chr15:73924400-73926200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:73924400-73926200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:73924400-73926200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr15:73924400-73926200	Active TSS	Placenta Amnion	Placenta Amnion
50	chr15:73924400-73926200	Active TSS	Small Intestine	intestine

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