Variant report

Variant	rs60916588
Chromosome Location	chr3:52570765-52570766
allele	C/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	TCF12	chr3:52570243-52571388	ECC-1	luminal epithelium:	n/a	n/a
7	KAP1	chr3:52570648-52571141	U2OS	brain:	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	TCF12	chr3:52570525-52570919	A549	lung:	n/a	n/a
12	PAX5	chr3:52570417-52570875	GM12878	blood:	n/a	n/a
13	GTF2F1	chr3:52570137-52571617	Hela-S3	cervix:	n/a	n/a
14	ZBTB33	chr3:52570435-52570920	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:52570124-52571517	GM12891	blood:	n/a	n/a
16	TAF1	chr3:52570386-52571195	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr3:52569563-52572387	IMR90	lung:	n/a	n/a
18	POU2F2	chr3:52570529-52570843	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:52570144-52571372	HCT-116	colon:	n/a	n/a
20	RUNX3	chr3:52570478-52571274	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:52570169-52571555	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr3:52569984-52571789	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr3:52570213-52571419	Hela-S3	cervix:	n/a	n/a
24	TBP	chr3:52570256-52571495	K562	blood:	n/a	n/a
25	YY1	chr3:52570195-52571013	HepG2	liver:	n/a	chr3:52570338-52570348 chr3:52570331-52570350 chr3:52570336-52570348 chr3:52570338-52570348 chr3:52570477-52570491
26	FOS	chr3:52570285-52570782	K562	blood:	n/a	chr3:52570571-52570580 chr3:52570538-52570547
27	TAF1	chr3:52570421-52571043	A549	lung:	n/a	n/a
28	CHD2	chr3:52570364-52571264	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:52570246-52571229	K562	blood:	n/a	n/a
30	EBF1	chr3:52570672-52570836	GM12878	blood:	n/a	n/a
31	REST	chr3:52570527-52570951	SK-N-SH	brain:	n/a	n/a
32	MYC	chr3:52570051-52571317	MCF10A-Er-Src	breast:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
33	REST	chr3:52570506-52570808	Hela-S3	cervix:	n/a	n/a
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	POLR2A	chr3:52570003-52572448	SK-N-MC	brain:	n/a	n/a
38	BHLHE40	chr3:52570252-52571350	HepG2	liver:	n/a	chr3:52571143-52571152 chr3:52571137-52571158 chr3:52571143-52571152
39	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
40	POLR2A	chr3:52570142-52570983	SK-N-MC	brain:	n/a	n/a
41	ELK4	chr3:52570444-52570879	Hela-S3	cervix:	n/a	n/a
42	ETS1	chr3:52570482-52570835	K562	blood:	n/a	n/a
43	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
44	POLR2A	chr3:52570291-52570873	A549	lung:	n/a	n/a
45	MAX	chr3:52569994-52571506	HCT-116	colon:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
46	POLR2A	chr3:52570185-52571505	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr3:52570475-52570815	A549	lung:	n/a	n/a
48	POLR2A	chr3:52570409-52572419	HepG2	liver:	n/a	n/a
49	TBP	chr3:52570311-52571394	H1-hESC	embryonic stem cell:	n/a	n/a
50	WRNIP1	chr3:52570699-52571000	GM12878	blood:	n/a	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	chr3:52442891..52445847-chr3:52570573..52572369,2	K562	blood:
14	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
15	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
16	chr3:52510130..52511955-chr3:52570408..52572081,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5DC2-1	chr3:52570621-52571075	ENSG00000245797

Variant related genes	Relation type
NT5DC2	TF binding region
ENSG00000163930	Chromatin interaction
ENSG00000252768	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000255198	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	chr3:52569000-52571200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:52569200-52571000	Active TSS	Fetal Brain Female	brain
4	chr3:52569200-52571200	Active TSS	Brain Germinal Matrix	brain
5	chr3:52570000-52571400	Active TSS	Psoas Muscle	Psoas
6	chr3:52570000-52571800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:52570000-52573600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr3:52570200-52571000	Active TSS	Primary T cells from cord blood	blood
9	chr3:52570200-52571000	Active TSS	Brain Angular Gyrus	brain
10	chr3:52570200-52571000	Active TSS	Placenta	Placenta
11	chr3:52570200-52571000	Active TSS	Placenta Amnion	Placenta Amnion
12	chr3:52570200-52571000	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr3:52570200-52571000	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:52570200-52571200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:52570200-52571200	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr3:52570200-52571200	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr3:52570200-52571200	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:52570200-52571200	Active TSS	Brain Anterior Caudate	brain
19	chr3:52570200-52571200	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:52570200-52571200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:52570200-52571200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:52570200-52571200	Active TSS	Brain Substantia Nigra	brain
23	chr3:52570200-52571200	Active TSS	Stomach Mucosa	stomach
24	chr3:52570200-52571200	Active TSS	Thymus	Thymus
25	chr3:52570200-52571200	Active TSS	Osteobl	bone
26	chr3:52570200-52571400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:52570200-52571400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52570200-52571400	Active TSS	Colonic Mucosa	Colon
29	chr3:52570200-52571400	Active TSS	Colon Smooth Muscle	Colon
30	chr3:52570200-52571400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:52570200-52571400	Active TSS	Fetal Intestine Large	intestine
32	chr3:52570200-52571600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr3:52570200-52571800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:52570200-52571800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:52570200-52571800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:52570200-52571800	Active TSS	Aorta	Aorta
37	chr3:52570200-52571800	Active TSS	Fetal Intestine Small	intestine
38	chr3:52570200-52571800	Active TSS	Ovary	ovary
39	chr3:52570200-52571800	Active TSS	Pancreas	Pancrea
40	chr3:52570200-52571800	Active TSS	Right Atrium	heart
41	chr3:52570200-52571800	Active TSS	Right Ventricle	heart
42	chr3:52570200-52572000	Active TSS	A549	lung
43	chr3:52570200-52572400	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:52570400-52570800	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr3:52570400-52570800	Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr3:52570400-52570800	Active TSS	Primary B cells from cord blood	blood
47	chr3:52570400-52570800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:52570400-52570800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr3:52570400-52570800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52570400-52570800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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