Variant report

Variant	rs58924550
Chromosome Location	chr3:52570496-52570497
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	CHD2	chr3:52570126-52571419	GM12878	blood:	n/a	n/a
2	EP300	chr3:52570258-52570834	GM12878	blood:	n/a	chr3:52570552-52570568 chr3:52570604-52570620
3	EGR1	chr3:52570150-52570859	ECC-1	luminal epithelium:	n/a	chr3:52570555-52570568 chr3:52570556-52570566 chr3:52570555-52570568 chr3:52570556-52570566 chr3:52570555-52570568 chr3:52570556-52570565 chr3:52570552-52570566 chr3:52570555-52570568 chr3:52570475-52570484
4	POLR2A	chr3:52570199-52571273	GM19193	blood:	n/a	n/a
5	POLR2A	chr3:52570214-52571578	GM12878	blood:	n/a	n/a
6	NRF1	chr3:52570260-52570761	GM12878	blood:	n/a	chr3:52570358-52570367 chr3:52570474-52570485
7	TCF12	chr3:52570243-52571388	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr3:52570130-52571316	MCF10A-Er-Src	breast:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
9	POLR2A	chr3:52570249-52571325	MCF-7	breast:	n/a	n/a
10	SIN3AK20	chr3:52570471-52570873	HepG2	liver:	n/a	n/a
11	FOS	chr3:52570284-52570745	GM12878	blood:	n/a	chr3:52570571-52570580 chr3:52570538-52570547
12	ATF3	chr3:52570296-52570590	K562	blood:	n/a	n/a
13	PAX5	chr3:52570417-52570875	GM12878	blood:	n/a	n/a
14	GTF2F1	chr3:52570137-52571617	Hela-S3	cervix:	n/a	n/a
15	ZBTB33	chr3:52570435-52570920	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:52570124-52571517	GM12891	blood:	n/a	n/a
17	USF2	chr3:52570179-52570691	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr3:52570386-52571195	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF1	chr3:52570215-52570709	HepG2	liver:	n/a	chr3:52570423-52570434
20	JUND	chr3:52570382-52570721	HepG2	liver:	n/a	chr3:52570571-52570580 chr3:52570538-52570547
21	MXI1	chr3:52569563-52572387	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:52570144-52571372	HCT-116	colon:	n/a	n/a
23	RUNX3	chr3:52570478-52571274	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:52570169-52571555	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:52569984-52571789	MCF10A-Er-Src	breast:	n/a	n/a
26	MXI1	chr3:52570213-52571419	Hela-S3	cervix:	n/a	n/a
27	TBP	chr3:52570256-52571495	K562	blood:	n/a	n/a
28	YY1	chr3:52570195-52571013	HepG2	liver:	n/a	chr3:52570338-52570348 chr3:52570331-52570350 chr3:52570336-52570348 chr3:52570338-52570348 chr3:52570477-52570491
29	FOS	chr3:52570285-52570782	K562	blood:	n/a	chr3:52570571-52570580 chr3:52570538-52570547
30	TAF1	chr3:52570421-52571043	A549	lung:	n/a	n/a
31	CHD2	chr3:52570364-52571264	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:52570246-52571229	K562	blood:	n/a	n/a
33	MYC	chr3:52570051-52571317	MCF10A-Er-Src	breast:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
34	PML	chr3:52570399-52570926	K562	blood:	n/a	n/a
35	CHD2	chr3:52570181-52571208	K562	blood:	n/a	n/a
36	SIN3A	chr3:52570280-52571176	GM12878	blood:	n/a	chr3:52570478-52570491
37	USF1	chr3:52570168-52570647	A549	lung:	n/a	chr3:52570423-52570434
38	POLR2A	chr3:52570003-52572448	SK-N-MC	brain:	n/a	n/a
39	BHLHE40	chr3:52570252-52571350	HepG2	liver:	n/a	chr3:52571143-52571152 chr3:52571137-52571158 chr3:52571143-52571152
40	USF1	chr3:52570092-52571428	SK-N-SH	brain:	n/a	chr3:52571143-52571152 chr3:52571110-52571121 chr3:52571137-52571158 chr3:52571143-52571152 chr3:52570423-52570434 chr3:52571141-52571152
41	POLR2A	chr3:52570142-52570983	SK-N-MC	brain:	n/a	n/a
42	YY1	chr3:52570112-52570514	H1-hESC	embryonic stem cell:	n/a	chr3:52570338-52570348 chr3:52570331-52570350 chr3:52570336-52570348 chr3:52570338-52570348 chr3:52570477-52570491
43	ELK4	chr3:52570444-52570879	Hela-S3	cervix:	n/a	n/a
44	ETS1	chr3:52570482-52570835	K562	blood:	n/a	n/a
45	NFYA	chr3:52570275-52570878	K562	blood:	n/a	chr3:52570537-52570551 chr3:52570569-52570584 chr3:52570532-52570550 chr3:52570540-52570552 chr3:52570536-52570551 chr3:52570536-52570551 chr3:52570572-52570582 chr3:52570565-52570583 chr3:52570539-52570549
46	POLR2A	chr3:52570291-52570873	A549	lung:	n/a	n/a
47	MAX	chr3:52569994-52571506	HCT-116	colon:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
48	POLR2A	chr3:52570185-52571505	GM12878	blood:	n/a	n/a
49	SIN3AK20	chr3:52570475-52570815	A549	lung:	n/a	n/a
50	POLR2A	chr3:52570409-52572419	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52570476-52570526	Jurkat	blood:	n/a
2	chr3:52570476-52570526	HL-60	blood:	n/a
3	chr3:52570476-52570526	AG09319	gingival:	n/a
4	chr3:52570476-52570526	MCF10A-Er-Src	breast:	n/a
5	chr3:52570476-52570526	Caco-2	colon:	n/a
6	chr3:52570476-52570526	HCF	heart:	n/a
7	chr3:52570476-52570526	AoSMC	blood vessel:	n/a
8	chr3:52570476-52570526	AG04449	skin:	fetal
9	chr3:52570476-52570526	SK-N-SH	brain:	n/a
10	chr3:52570476-52570526	GM12891	blood:	n/a
11	chr3:52570476-52570526	HEEpiC	esophagus:	n/a
12	chr3:52570476-52570526	GM12892	blood:	n/a
13	chr3:52570476-52570526	LNCaP	prostate:	n/a
14	chr3:52570476-52570526	NHBE	bronchial:	n/a
15	chr3:52570476-52570526	HepG2	liver:	n/a
16	chr3:52570476-52570526	HUVEC	blood vessel:	n/a
17	chr3:52570476-52570526	GM06990	blood:	n/a
18	chr3:52570476-52570526	A549	lung:	n/a
19	chr3:52570476-52570526	AG04450	lung:	fetal
20	chr3:52570476-52570526	HIPEpiC	eye:	n/a
21	chr3:52570476-52570526	GM12878	blood:	n/a
22	chr3:52570476-52570526	NB4	blood:	n/a
23	chr3:52570476-52570526	HCPEpiC	choroid plexus:	n/a
24	chr3:52570476-52570526	ovcar-3	ovarian:	n/a
25	chr3:52570476-52570526	K562	blood:	n/a
26	chr3:52570476-52570526	Hela-S3	cervix:	n/a
27	chr3:52570476-52570526	RPTEC	kidney:	n/a
28	chr3:52570476-52570526	ProgFib	skin:	n/a
29	chr3:52570476-52570526	HRCEpiC	kidney:	n/a
30	chr3:52570476-52570526	NHDF-neo	bronchial:	n/a
31	chr3:52570476-52570526	SK-N-MC	brain:	n/a
32	chr3:52570476-52570526	HEK293	kidney:	embryo
33	chr3:52570476-52570526	BJ	skin:	n/a
34	chr3:52570476-52570526	IMR90	lung:	fetal
35	chr3:52570476-52570526	PrEC	prostate:	n/a
36	chr3:52570476-52570526	HCM	heart:	n/a
37	chr3:52570476-52570526	SKMC	muscle:	n/a
38	chr3:52570476-52570526	PANC-1	pancreas:	n/a
39	chr3:52570476-52570526	SK-N-SH_RA	brain:	n/a
40	chr3:52570476-52570526	Hepatocyte	liver:	n/a
41	chr3:52570476-52570526	U87	brain:	n/a
42	chr3:52570476-52570526	NH-A	brain:	n/a
43	chr3:52570476-52570526	GM19239	blood:	n/a
44	chr3:52570476-52570526	SAEC	small airway:	n/a
45	chr3:52570476-52570526	HAEpiC	amniotic membrane:	n/a
46	chr3:52570476-52570526	AG09309	skin:	n/a
47	chr3:52570476-52570526	CMK	blood:	n/a
48	chr3:52570476-52570526	NT2-D1	testis:	n/a
49	chr3:52570476-52570526	HRE	kidney:	n/a
50	chr3:52570476-52570526	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52569931..52572827-chr3:52736282..52738188,2	K562	blood:
2	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
3	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
4	chr3:52541629..52544116-chr3:52570482..52572184,2	MCF-7	breast:
5	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
6	chr16:2014433..2014972-chr3:52569933..52570806,2	NB4	blood:
7	chr11:47869648..47870294-chr3:52570367..52571073,2	HCT-116	colon:
8	chr3:52570222..52571915-chr3:52739151..52740818,2	MCF-7	breast:
9	chr3:52569842..52571498-chr3:52584728..52587706,2	MCF-7	breast:
10	chr2:48010056..48010954-chr3:52570382..52571267,2	Hela-S3	cervix:
11	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
12	chr1:150337113..150338018-chr3:52570346..52571261,2	Hela-S3	cervix:
13	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
14	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
15	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
16	chr3:52510130..52511955-chr3:52570408..52572081,2	MCF-7	breast:

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
SMIM4	CpG island
NT5DC2	CpG island
ENSG00000010327	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000252768	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510759	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12107484	0.85[AFR][1000 genomes]
rs1987234	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34173244	0.86[AFR][1000 genomes]
rs35920544	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs56259931	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57246324	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57298447	0.86[AFR][1000 genomes]
rs57319306	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57560655	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57757646	0.85[AFR][1000 genomes]
rs57869735	0.86[AFR][1000 genomes]
rs58100002	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58725214	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs59078569	1.00[ASN][1000 genomes]
rs59410274	1.00[ASN][1000 genomes]
rs60311166	0.83[AFR][1000 genomes]
rs60415551	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60611300	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60682984	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60823713	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60916588	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61418167	1.00[ASN][1000 genomes]
rs61538294	0.81[AFR][1000 genomes]
rs6774097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780005	0.81[AFR][1000 genomes]
rs6803492	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947535	0.91[AFR][1000 genomes]
rs72947580	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72947589	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72950430	0.81[AFR][1000 genomes]
rs72965177	0.85[AFR][1000 genomes]
rs72965181	0.88[AFR][1000 genomes]
rs7643568	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647992	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7648016	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr3:52566200-52571600	Active TSS	Fetal Kidney	kidney
2	chr3:52568200-52570600	Weak transcription	Small Intestine	intestine
3	chr3:52568600-52570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52568600-52570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52568600-52570600	Weak transcription	HSMMtube	muscle
6	chr3:52568800-52570600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:52569000-52570600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:52569000-52570600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52569000-52570600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52569000-52570600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52569000-52570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:52569000-52570600	Weak transcription	Gastric	stomach
13	chr3:52569000-52570600	Weak transcription	Left Ventricle	heart
14	chr3:52569000-52570600	Weak transcription	Lung	lung
15	chr3:52569000-52570600	Weak transcription	Spleen	Spleen
16	chr3:52569000-52570600	Enhancers	HUVEC	blood vessel
17	chr3:52569000-52571200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:52569200-52570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:52569200-52571000	Active TSS	Fetal Brain Female	brain
20	chr3:52569200-52571200	Active TSS	Brain Germinal Matrix	brain
21	chr3:52569400-52570600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:52569600-52570600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:52569800-52570600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:52570000-52570600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:52570000-52570600	Weak transcription	Esophagus	oesophagus
26	chr3:52570000-52571400	Active TSS	Psoas Muscle	Psoas
27	chr3:52570000-52571800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:52570000-52573600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:52570200-52570600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:52570200-52570600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:52570200-52570600	Enhancers	Fetal Heart	heart
32	chr3:52570200-52571000	Active TSS	Primary T cells from cord blood	blood
33	chr3:52570200-52571000	Active TSS	Brain Angular Gyrus	brain
34	chr3:52570200-52571000	Active TSS	Placenta	Placenta
35	chr3:52570200-52571000	Active TSS	Placenta Amnion	Placenta Amnion
36	chr3:52570200-52571000	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr3:52570200-52571000	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:52570200-52571200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:52570200-52571200	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:52570200-52571200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr3:52570200-52571200	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr3:52570200-52571200	Active TSS	Brain Anterior Caudate	brain
43	chr3:52570200-52571200	Active TSS	Brain Cingulate Gyrus	brain
44	chr3:52570200-52571200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:52570200-52571200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:52570200-52571200	Active TSS	Brain Substantia Nigra	brain
47	chr3:52570200-52571200	Active TSS	Stomach Mucosa	stomach
48	chr3:52570200-52571200	Active TSS	Thymus	Thymus
49	chr3:52570200-52571200	Active TSS	Osteobl	bone
50	chr3:52570200-52571400	Active TSS	HUES6 Cell Line	embryonic stem cell

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