Variant report

Variant	rs66782572
Chromosome Location	chr3:52567617-52567618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52567570-52567882	HepG2	liver:	n/a	n/a
2	YY1	chr3:52567391-52568185	ECC-1	luminal epithelium:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
3	NFYB	chr3:52567559-52568304	GM12878	blood:	n/a	chr3:52567864-52567879 chr3:52567861-52567876 chr3:52567864-52567879 chr3:52567864-52567878
4	POLR2A	chr3:52566966-52567850	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:52566536-52568278	GM15510	blood:	n/a	n/a
6	POLR2A	chr3:52567449-52568224	HEK293	kidney:	n/a	n/a
7	CHD2	chr3:52567513-52568198	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52567579-52567842	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:52567605-52567900	A549	lung:	n/a	n/a
10	POLR2A	chr3:52567427-52568232	GM18505	blood:	n/a	n/a
11	MAX	chr3:52567337-52569379	HepG2	liver:	n/a	n/a
12	MXI1	chr3:52566450-52569219	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:52567556-52567835	HCT-116	colon:	n/a	n/a
14	POLR2A	chr3:52566494-52568343	GM12892	blood:	n/a	n/a
15	MAX	chr3:52567368-52568098	NB4	blood:	n/a	n/a
16	CCNT2	chr3:52566580-52568816	K562	blood:	n/a	chr3:52566977-52566986 chr3:52567974-52567983 chr3:52567185-52567194 chr3:52567981-52567990
17	UBTF	chr3:52566770-52567678	K562	blood:	n/a	n/a
18	EGR1	chr3:52567555-52567852	GM12878	blood:	n/a	n/a
19	HMGN3	chr3:52566706-52568905	K562	blood:	n/a	n/a
20	MAZ	chr3:52567452-52568161	Hela-S3	cervix:	n/a	n/a
21	HA-E2F1	chr3:52567385-52568072	Hela-S3	cervix:	n/a	n/a
22	NFYA	chr3:52567550-52568021	Hela-S3	cervix:	n/a	chr3:52567864-52567879 chr3:52567864-52567879 chr3:52567864-52567878
23	MAX	chr3:52567064-52568083	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:52567502-52568210	NB4	blood:	n/a	n/a
25	POLR2A	chr3:52567417-52568187	Gliobla	brain:	n/a	n/a
26	E2F6	chr3:52567290-52569157	K562	blood:	n/a	n/a
27	POLR2A	chr3:52566562-52568130	GM12878	blood:	n/a	n/a
28	PBX3	chr3:52567550-52567941	A549	lung:	n/a	chr3:52567867-52567876
29	TCF3	chr3:52567376-52567819	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:52567422-52568418	MCF-7	breast:	n/a	n/a
31	TAF1	chr3:52567378-52568288	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:52565761-52567641	U87	brain:	n/a	n/a
33	UBTF	chr3:52566448-52567664	K562	blood:	n/a	n/a
34	MAX	chr3:52567242-52567631	A549	lung:	n/a	n/a
35	POLR2A	chr3:52567367-52567909	Hela-S3	cervix:	n/a	n/a
36	HEY1	chr3:52567525-52567776	K562	blood:	n/a	n/a
37	ZBTB7A	chr3:52567016-52568425	ECC-1	luminal epithelium:	n/a	chr3:52568173-52568181
38	MAX	chr3:52567066-52568226	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:52566714-52569188	MCF-7	breast:	n/a	n/a
40	MAX	chr3:52567313-52569354	HepG2	liver:	n/a	n/a
41	MAX	chr3:52567187-52568696	A549	lung:	n/a	n/a
42	POLR2A	chr3:52567370-52567929	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr3:52567446-52568195	Raji	blood:	n/a	n/a
44	POLR2A	chr3:52567562-52568247	GM18526	blood:	n/a	n/a
45	E2F6	chr3:52567435-52567710	K562	blood:	n/a	n/a
46	CHD2	chr3:52567348-52568163	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr3:52567330-52567917	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr3:52567407-52567906	HUVEC	blood vessel:	n/a	n/a
49	HEY1	chr3:52567542-52568299	HepG2	liver:	n/a	n/a
50	ZBTB7A	chr3:52567147-52567720	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52567604-52567654	HEEpiC	esophagus:	n/a
2	chr3:52567604-52567654	SK-N-SH_RA	brain:	n/a
3	chr3:52567604-52567654	HAEpiC	amniotic membrane:	n/a
4	chr3:52567604-52567654	GM06990	blood:	n/a
5	chr3:52567604-52567654	AG09319	gingival:	n/a
6	chr3:52567604-52567654	AG04449	skin:	fetal
7	chr3:52567604-52567654	IMR90	lung:	fetal
8	chr3:52567604-52567654	MCF10A-Er-Src	breast:	n/a
9	chr3:52567604-52567654	NB4	blood:	n/a
10	chr3:52567604-52567654	SKMC	muscle:	n/a
11	chr3:52567604-52567654	K562	blood:	n/a
12	chr3:52567604-52567654	GM12878	blood:	n/a
13	chr3:52567604-52567654	HCPEpiC	choroid plexus:	n/a
14	chr3:52567604-52567654	GM12891	blood:	n/a
15	chr3:52567604-52567654	PFSK-1	brain:	n/a
16	chr3:52567604-52567654	Hepatocyte	liver:	n/a
17	chr3:52567604-52567654	HEK293	kidney:	embryo
18	chr3:52567604-52567654	HCF	heart:	n/a
19	chr3:52567604-52567654	A549	lung:	n/a
20	chr3:52567604-52567654	ECC-1	luminal epithelium:	n/a
21	chr3:52567604-52567654	SAEC	small airway:	n/a
22	chr3:52567604-52567654	ovcar-3	ovarian:	n/a
23	chr3:52567604-52567654	ProgFib	skin:	n/a
24	chr3:52567604-52567654	MCF-7	breast:	n/a
25	chr3:52567604-52567654	BE2_C	brain:	n/a
26	chr3:52567604-52567654	CMK	blood:	n/a
27	chr3:52567604-52567654	HPAEpiC	pulmonary alveolar:	n/a
28	chr3:52567604-52567654	AG09309	skin:	n/a
29	chr3:52567604-52567654	PANC-1	pancreas:	n/a
30	chr3:52567604-52567654	HCM	heart:	n/a
31	chr3:52567604-52567654	AoSMC	blood vessel:	n/a
32	chr3:52567604-52567654	U87	brain:	n/a
33	chr3:52567604-52567654	SK-N-MC	brain:	n/a
34	chr3:52567604-52567654	T-47D	breast:	n/a
35	chr3:52567604-52567654	HRCEpiC	kidney:	n/a
36	chr3:52567604-52567654	H1-hESC	embryonic stem cell:	embryo
37	chr3:52567604-52567654	HL-60	blood:	n/a
38	chr3:52567604-52567654	NHBE	bronchial:	n/a
39	chr3:52567604-52567654	HMEC	breast:	n/a
40	chr3:52567604-52567654	NHDF-neo	bronchial:	n/a
41	chr3:52567604-52567654	PrEC	prostate:	n/a
42	chr3:52567604-52567654	Jurkat	blood:	n/a
43	chr3:52567604-52567654	Caco-2	colon:	n/a
44	chr3:52567604-52567654	HCT-116	colon:	n/a
45	chr3:52567604-52567654	Hela-S3	cervix:	n/a
46	chr3:52567604-52567654	HepG2	liver:	n/a
47	chr3:52567604-52567654	HRPEpiC	eye:	n/a
48	chr3:52567604-52567654	HRE	kidney:	n/a
49	chr3:52567604-52567654	BJ	skin:	n/a
50	chr3:52567604-52567654	HNPCEpiC	eye:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
2	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
3	chr3:52567230..52568070-chr9:131218351..131218852,2	Hela-S3	cervix:
4	chr3:52567015..52567802-chr3:186500888..186501659,2	Hela-S3	cervix:
5	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
6	chr3:52566165..52568026-chr3:52648479..52651083,2	K562	blood:
7	chr15:65596638..65597519-chr3:52567379..52568024,2	HCT-116	colon:
8	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:
9	chr3:52551484..52554158-chr3:52567066..52569157,2	MCF-7	breast:
10	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
11	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
12	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
13	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
14	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
15	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:
16	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
17	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:

No data

Variant related genes	Relation type
NT5DC2	TF binding region
SMIM4	TF binding region
SMIM4	CpG island
NT5DC2	CpG island
ENSG00000114854	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000136811	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000156976	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1010553	0.82[EUR][1000 genomes]
rs1010554	0.85[EUR][1000 genomes]
rs11130306	0.83[EUR][1000 genomes]
rs1133415	0.82[ASN][1000 genomes]
rs11709284	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489732	0.83[ASN][1000 genomes]
rs12489828	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13076398	0.83[ASN][1000 genomes]
rs13081028	0.82[EUR][1000 genomes]
rs13303	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13621	0.81[ASN][1000 genomes]
rs1570	0.81[ASN][1000 genomes]
rs17052256	0.81[ASN][1000 genomes]
rs17052259	0.81[ASN][1000 genomes]
rs1961959	0.80[ASN][1000 genomes]
rs2289249	0.81[ASN][1000 genomes]
rs28661185	0.82[ASN][1000 genomes]
rs2878628	0.81[ASN][1000 genomes]
rs33964154	0.81[ASN][1000 genomes]
rs34005367	0.82[ASN][1000 genomes]
rs3796353	0.81[ASN][1000 genomes]
rs4282054	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4475032	0.82[ASN][1000 genomes]
rs4687625	0.82[ASN][1000 genomes]
rs4687626	0.83[ASN][1000 genomes]
rs62256903	0.83[ASN][1000 genomes]
rs6445528	0.82[ASN][1000 genomes]
rs66824127	0.82[EUR][1000 genomes]
rs6778735	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6778844	0.81[ASN][1000 genomes]
rs7614981	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7636227	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7638808	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	esv3389739	chr3:52566962-52569135	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv11293	chr3:52567550-52568100	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66782572	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52566200-52569000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:52566200-52571600	Active TSS	Fetal Kidney	kidney
3	chr3:52566400-52568600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52566400-52568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52566400-52569000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:52566600-52567800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:52566600-52567800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:52566600-52568400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:52566600-52568400	Active TSS	Brain Angular Gyrus	brain
10	chr3:52566600-52568600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:52566600-52568600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:52566600-52568600	Active TSS	A549	lung
13	chr3:52566600-52568800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:52566800-52568200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:52566800-52568200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr3:52566800-52568400	Active TSS	NH-A	brain
17	chr3:52566800-52568600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr3:52566800-52568600	Active TSS	HSMMtube	muscle
19	chr3:52566800-52568800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr3:52566800-52568800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:52566800-52568800	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:52566800-52569000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:52566800-52569200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:52566800-52569200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52566800-52569400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:52567000-52567800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:52567000-52568000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:52567000-52568200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52567000-52568200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:52567000-52568200	Active TSS	Primary T cells from cord blood	blood
31	chr3:52567000-52568200	Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:52567000-52568200	Active TSS	Brain Anterior Caudate	brain
33	chr3:52567000-52568200	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:52567000-52568200	Active TSS	Esophagus	oesophagus
35	chr3:52567000-52568200	Active TSS	Fetal Stomach	stomach
36	chr3:52567000-52568200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:52567000-52568200	Active TSS	Small Intestine	intestine
38	chr3:52567000-52568200	Active TSS	GM12878-XiMat	blood
39	chr3:52567000-52568200	Active TSS	Hela-S3	cervix
40	chr3:52567000-52568200	Active TSS	HepG2	liver
41	chr3:52567000-52568200	Active TSS	HUVEC	blood vessel
42	chr3:52567000-52568200	Active TSS	Osteobl	bone
43	chr3:52567000-52568400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:52567000-52568400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:52567000-52568400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52567000-52568400	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:52567000-52568400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:52567000-52568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:52567000-52568400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52567000-52568400	Active TSS	Brain Cingulate Gyrus	brain

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