Variant report

Variant	rs7628665
Chromosome Location	chr3:52568225-52568226
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:94)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:94 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:52567694-52568280	A549	lung:	n/a	n/a
2	POLR2A	chr3:52567801-52568278	HUVEC	blood vessel:	n/a	n/a
3	TAF1	chr3:52567823-52568240	ECC-1	luminal epithelium:	n/a	n/a
4	ELF1	chr3:52567793-52568333	GM12878	blood:	n/a	chr3:52567885-52567897
5	NFYB	chr3:52567559-52568304	GM12878	blood:	n/a	chr3:52567864-52567879 chr3:52567861-52567876 chr3:52567864-52567879 chr3:52567864-52567878
6	YY1	chr3:52567786-52568597	HepG2	liver:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
7	POLR2A	chr3:52566536-52568278	GM15510	blood:	n/a	n/a
8	POLR2A	chr3:52567801-52568351	HUVEC	blood vessel:	n/a	n/a
9	UBTF	chr3:52567975-52568263	K562	blood:	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	chr3:52566494-52568343	GM12892	blood:	n/a	n/a
14	CCNT2	chr3:52566580-52568816	K562	blood:	n/a	chr3:52566977-52566986 chr3:52567974-52567983 chr3:52567185-52567194 chr3:52567981-52567990
15	ETS1	chr3:52567814-52568262	K562	blood:	n/a	chr3:52567981-52567992
16	YY1	chr3:52567823-52568262	SK-N-SH_RA	brain:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
17	NFIC	chr3:52567790-52568229	ECC-1	luminal epithelium:	n/a	n/a
18	GABPA	chr3:52567933-52568294	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZBTB7A	chr3:52567786-52568295	K562	blood:	n/a	chr3:52568173-52568181
20	HMGN3	chr3:52566706-52568905	K562	blood:	n/a	n/a
21	JUN	chr3:52567828-52568317	K562	blood:	n/a	n/a
22	POLR2A	chr3:52567956-52568519	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:52567962-52568249	HepG2	liver:	n/a	n/a
24	E2F6	chr3:52567290-52569157	K562	blood:	n/a	n/a
25	POLR2A	chr3:52567422-52568418	MCF-7	breast:	n/a	n/a
26	YY1	chr3:52567835-52568273	GM12878	blood:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
27	TAF1	chr3:52567378-52568288	HepG2	liver:	n/a	n/a
28	GABPA	chr3:52567927-52568251	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr3:52567700-52568511	SK-N-SH	brain:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
30	MYC	chr3:52567759-52568375	K562	blood:	n/a	n/a
31	POLR2A	chr3:52567909-52568345	HUVEC	blood vessel:	n/a	n/a
32	ZBTB7A	chr3:52567016-52568425	ECC-1	luminal epithelium:	n/a	chr3:52568173-52568181
33	MAX	chr3:52567066-52568226	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZNF263	chr3:52567993-52568474	HEK293-T-REx	kidney:	n/a	n/a
35	POLR2A	chr3:52567937-52568390	U87	brain:	n/a	n/a
36	NFYA	chr3:52567842-52568304	K562	blood:	n/a	chr3:52567864-52567879 chr3:52567864-52567879 chr3:52567864-52567878
37	POLR2A	chr3:52566714-52569188	MCF-7	breast:	n/a	n/a
38	MAX	chr3:52567313-52569354	HepG2	liver:	n/a	n/a
39	MAX	chr3:52567187-52568696	A549	lung:	n/a	n/a
40	MAX	chr3:52567951-52569156	HepG2	liver:	n/a	n/a
41	ATF2	chr3:52567800-52568226	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:52567562-52568247	GM18526	blood:	n/a	n/a
43	YY1	chr3:52567842-52568271	SK-N-SH_RA	brain:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
44	YY1	chr3:52567854-52568245	H1-hESC	embryonic stem cell:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
45	HEY1	chr3:52567542-52568299	HepG2	liver:	n/a	n/a
46	E2F6	chr3:52567731-52568630	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:52566584-52568241	GM18951	blood:	n/a	n/a
48	GTF2F1	chr3:52568061-52568334	H1-hESC	embryonic stem cell:	n/a	n/a
49	PBX3	chr3:52567567-52568288	SK-N-SH	brain:	n/a	chr3:52567867-52567876
50	ELF1	chr3:52567804-52568293	GM12878	blood:	n/a	chr3:52567885-52567897

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52568218-52568268	H1-hESC	embryonic stem cell:	embryo
2	chr3:52568218-52568268	NB4	blood:	n/a
3	chr3:52568218-52568268	NHDF-neo	bronchial:	n/a
4	chr3:52568218-52568268	Hela-S3	cervix:	n/a
5	chr3:52568218-52568268	Caco-2	colon:	n/a
6	chr3:52568218-52568268	BE2_C	brain:	n/a
7	chr3:52568218-52568268	HRPEpiC	eye:	n/a
8	chr3:52568218-52568268	HCM	heart:	n/a
9	chr3:52568218-52568268	SKMC	muscle:	n/a
10	chr3:52568218-52568268	LNCaP	prostate:	n/a
11	chr3:52568218-52568268	AG04450	lung:	fetal
12	chr3:52568218-52568268	HAEpiC	amniotic membrane:	n/a
13	chr3:52568218-52568268	HIPEpiC	eye:	n/a
14	chr3:52568218-52568268	SK-N-MC	brain:	n/a
15	chr3:52568218-52568268	A549	lung:	n/a
16	chr3:52568218-52568268	AG04449	skin:	fetal
17	chr3:52568218-52568268	MCF-7	breast:	n/a
18	chr3:52568218-52568268	RPTEC	kidney:	n/a
19	chr3:52568218-52568268	SK-N-SH	brain:	n/a
20	chr3:52568218-52568268	CMK	blood:	n/a
21	chr3:52568218-52568268	AG10803	skin:	n/a
22	chr3:52568218-52568268	PFSK-1	brain:	n/a
23	chr3:52568218-52568268	U87	brain:	n/a
24	chr3:52568218-52568268	AoSMC	blood vessel:	n/a
25	chr3:52568218-52568268	HCF	heart:	n/a
26	chr3:52568218-52568268	ECC-1	luminal epithelium:	n/a
27	chr3:52568218-52568268	HRCEpiC	kidney:	n/a
28	chr3:52568218-52568268	HNPCEpiC	eye:	n/a
29	chr3:52568218-52568268	AG09309	skin:	n/a
30	chr3:52568218-52568268	NH-A	brain:	n/a
31	chr3:52568218-52568268	ProgFib	skin:	n/a
32	chr3:52568218-52568268	SAEC	small airway:	n/a
33	chr3:52568218-52568268	T-47D	breast:	n/a
34	chr3:52568218-52568268	K562	blood:	n/a
35	chr3:52568218-52568268	HPAEpiC	pulmonary alveolar:	n/a
36	chr3:52568218-52568268	PANC-1	pancreas:	n/a
37	chr3:52568218-52568268	Jurkat	blood:	n/a
38	chr3:52568218-52568268	HUVEC	blood vessel:	n/a
39	chr3:52568218-52568268	HEEpiC	esophagus:	n/a
40	chr3:52568218-52568268	PrEC	prostate:	n/a
41	chr3:52568218-52568268	HepG2	liver:	n/a
42	chr3:52568218-52568268	AG09319	gingival:	n/a
43	chr3:52568218-52568268	MCF10A-Er-Src	breast:	n/a
44	chr3:52568218-52568268	NHBE	bronchial:	n/a
45	chr3:52568218-52568268	NT2-D1	testis:	n/a
46	chr3:52568218-52568268	GM19239	blood:	n/a
47	chr3:52568218-52568268	GM12891	blood:	n/a
48	chr3:52568218-52568268	ovcar-3	ovarian:	n/a
49	chr3:52568218-52568268	Hepatocyte	liver:	n/a
50	chr3:52568218-52568268	HMEC	breast:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
2	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
3	chr22:47133970..47134516-chr3:52567792..52568293,2	HCT-116	colon:
4	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
5	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
6	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
7	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:
8	chr3:52551484..52554158-chr3:52567066..52569157,2	MCF-7	breast:
9	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
10	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
11	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
12	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
13	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
14	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:
15	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
16	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:

No data

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
SMIM4	CpG island
NT5DC2	CpG island
ENSG00000016864	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000100422	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

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	chr3:52566600-52568400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:52566600-52568400	Active TSS	Brain Angular Gyrus	brain
8	chr3:52566600-52568600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52566600-52568600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:52566600-52568600	Active TSS	A549	lung
11	chr3:52566600-52568800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:52566800-52568400	Active TSS	NH-A	brain
13	chr3:52566800-52568600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:52566800-52568600	Active TSS	HSMMtube	muscle
15	chr3:52566800-52568800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:52566800-52568800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:52566800-52568800	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:52566800-52569000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:52566800-52569200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:52566800-52569200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:52566800-52569400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:52567000-52568400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr3:52567000-52568400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:52567000-52568400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52567000-52568400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:52567000-52568400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52567000-52568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:52567000-52568400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:52567000-52568400	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:52567000-52568400	Weak transcription	Fetal Heart	heart
31	chr3:52567000-52568400	Active TSS	K562	blood
32	chr3:52567000-52568400	Active TSS	NHEK	skin
33	chr3:52567000-52568600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:52567000-52568600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:52567000-52568600	Active TSS	Brain Hippocampus Middle	brain
36	chr3:52567000-52568600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52567000-52568600	Active TSS	Brain Substantia Nigra	brain
38	chr3:52567000-52568600	Active TSS	Fetal Brain Female	brain
39	chr3:52567000-52568600	Active TSS	Ovary	ovary
40	chr3:52567000-52568600	Active TSS	NHDF-Ad	bronchial
41	chr3:52567000-52568800	Active TSS	Fetal Lung	lung
42	chr3:52567000-52568800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr3:52567000-52568800	Active TSS	Right Atrium	heart
44	chr3:52567000-52569000	Active TSS	Colon Smooth Muscle	Colon
45	chr3:52567000-52569200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr3:52567200-52568400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:52567200-52568400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:52567200-52568400	Active TSS	Fetal Intestine Small	intestine
49	chr3:52567200-52568400	Active TSS	Fetal Muscle Leg	muscle
50	chr3:52567200-52568400	Active TSS	Left Ventricle	heart

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