Variant report

Variant	rs4647002
Chromosome Location	chr1:59250093-59250094
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	CREB1	chr1:59248601-59251387	HepG2	liver:	n/a	chr1:59249776-59249789
2	ETS1	chr1:59249425-59250477	A549	lung:	n/a	chr1:59249668-59249681 chr1:59250315-59250324 chr1:59250314-59250327 chr1:59249820-59249831 chr1:59250313-59250324 chr1:59250315-59250324 chr1:59250313-59250323
3	POLR2A	chr1:59244106-59251818	U87	brain:	n/a	n/a
4	POLR2A	chr1:59245147-59251676	Hela-S3	cervix:	n/a	n/a
5	EP300	chr1:59249464-59251275	GM12878	blood:	n/a	chr1:59250255-59250264 chr1:59250260-59250276 chr1:59249576-59249590 chr1:59250316-59250323 chr1:59249489-59249505
6	MAX	chr1:59247473-59251323	GM12878	blood:	n/a	chr1:59249843-59249852
7	KAT2A	chr1:59249202-59250142	Hela-S3	cervix:	n/a	n/a
8	JUND	chr1:59249431-59250284	A549	lung:	n/a	chr1:59249778-59249787 chr1:59249798-59249807 chr1:59249822-59249831
9	POLR2A	chr1:59247151-59251494	GM12892	blood:	n/a	n/a
10	PML	chr1:59249416-59250191	GM12878	blood:	n/a	n/a
11	RELA	chr1:59249408-59251774	GM18951	blood:	n/a	n/a
12	HDAC2	chr1:59249533-59250219	MCF-7	breast:	n/a	chr1:59249585-59249599
13	POLR2A	chr1:59247671-59250698	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUN	chr1:59249066-59251132	K562	blood:	n/a	chr1:59251015-59251024 chr1:59249778-59249787 chr1:59249798-59249807 chr1:59250323-59250332 chr1:59249822-59249831 chr1:59250322-59250331 chr1:59249774-59249787
15	SP4	chr1:59249445-59250350	H1-hESC	embryonic stem cell:	n/a	chr1:59250319-59250335 chr1:59249822-59249833 chr1:59249818-59249834
16	EP300	chr1:59249546-59250546	ECC-1	luminal epithelium:	n/a	chr1:59250255-59250264 chr1:59250260-59250276 chr1:59249576-59249590 chr1:59250316-59250323
17	POLR2A	chr1:59243934-59251872	U87	brain:	n/a	n/a
18	CHD1	chr1:59244118-59252745	IMR90	lung:	n/a	chr1:59250203-59250213
19	POLR2A	chr1:59247234-59250280	H1-hESC	embryonic stem cell:	n/a	n/a
20	MYC	chr1:59249901-59250253	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:59249449-59251289	HCT-116	colon:	n/a	n/a
22	RCOR1	chr1:59248856-59251704	Hela-S3	cervix:	n/a	n/a
23	SRF	chr1:59249455-59250560	MCF-7	breast:	n/a	chr1:59249822-59249832
24	EP300	chr1:59249438-59250355	A549	lung:	n/a	chr1:59250255-59250264 chr1:59250260-59250276 chr1:59249576-59249590 chr1:59250316-59250323 chr1:59249489-59249505
25	ZBTB7A	chr1:59249798-59250489	K562	blood:	n/a	n/a
26	HEY1	chr1:59246437-59251188	K562	blood:	n/a	chr1:59250260-59250275 chr1:59249195-59249210
27	JUN	chr1:59249193-59251731	K562	blood:	n/a	chr1:59251015-59251024 chr1:59249778-59249787 chr1:59249798-59249807 chr1:59250323-59250332 chr1:59249822-59249831 chr1:59250322-59250331 chr1:59249774-59249787
28	ELF1	chr1:59249674-59251141	MCF-7	breast:	n/a	chr1:59250728-59250740 chr1:59250315-59250326 chr1:59250316-59250325 chr1:59250315-59250326 chr1:59250821-59250830 chr1:59250258-59250270
29	TCF12	chr1:59249489-59250100	A549	lung:	n/a	chr1:59249498-59249508
30	SP1	chr1:59249470-59250362	GM12878	blood:	n/a	chr1:59249822-59249834 chr1:59249822-59249833 chr1:59250320-59250334 chr1:59250324-59250333 chr1:59249824-59249833 chr1:59249823-59249832 chr1:59249789-59249810 chr1:59249822-59249834
31	POLR2A	chr1:59244614-59251725	HUVEC	blood vessel:	n/a	n/a
32	EP300	chr1:59248663-59251896	SK-N-SH	brain:	n/a	chr1:59250255-59250264 chr1:59249191-59249207 chr1:59249176-59249192 chr1:59250260-59250276 chr1:59251787-59251800 chr1:59249125-59249134 chr1:59249576-59249590 chr1:59250316-59250323 chr1:59249489-59249505
33	TCF12	chr1:59248641-59251958	SK-N-SH	brain:	n/a	chr1:59249475-59249485 chr1:59251331-59251338 chr1:59249498-59249508
34	CEBPB	chr1:59249566-59250239	IMR90	lung:	n/a	n/a
35	ZNF143	chr1:59249391-59250294	H1-hESC	embryonic stem cell:	n/a	chr1:59249417-59249435 chr1:59250021-59250036 chr1:59249670-59249688
36	JUND	chr1:59249499-59250288	A549	lung:	n/a	chr1:59249778-59249787 chr1:59249798-59249807 chr1:59249822-59249831
37	POLR2A	chr1:59247171-59251601	H1-hESC	embryonic stem cell:	n/a	n/a
38	TEAD4	chr1:59249870-59250113	H1-hESC	embryonic stem cell:	n/a	n/a
39	KAP1	chr1:59249484-59250164	U2OS	brain:	n/a	n/a
40	REST	chr1:59249481-59250174	SK-N-SH	brain:	n/a	chr1:59249842-59249851
41	GATA3	chr1:59249234-59251270	A549	lung:	n/a	chr1:59249740-59249752
42	ELF1	chr1:59249809-59250489	K562	blood:	n/a	chr1:59250315-59250326 chr1:59250316-59250325 chr1:59250315-59250326 chr1:59250258-59250270
43	REST	chr1:59249266-59250361	HL-60	blood:	n/a	chr1:59249842-59249851
44	MAZ	chr1:59249382-59251156	HepG2	liver:	n/a	chr1:59249843-59249852
45	TAF1	chr1:59249439-59250227	GM12891	blood:	n/a	n/a
46	TCF7L2	chr1:59249994-59250395	HEK293	kidney:	n/a	n/a
47	ZKSCAN1	chr1:59247347-59250548	Hela-S3	cervix:	n/a	n/a
48	POU2F2	chr1:59249390-59250262	GM12878	blood:	n/a	chr1:59250127-59250139
49	MAX	chr1:59247373-59250292	H1-hESC	embryonic stem cell:	n/a	chr1:59249843-59249852
50	POLR2A	chr1:59249146-59251081	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:59249779..59250379-chr9:95087142..95087891,2	Hela-S3	cervix:
2	chr1:46215764..46216413-chr1:59249299..59250095,2	Hela-S3	cervix:
3	chr1:59249695..59250360-chr18:61637493..61638045,2	Hela-S3	cervix:
4	chr1:52830101..52832396-chr1:59247801..59250793,2	K562	blood:
5	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
6	chr1:59249638..59250522-chr8:97247364..97248212,2	Hela-S3	cervix:
7	chr1:59249568..59250095-chr10:91404878..91405691,2	Hela-S3	cervix:
8	chr1:59245578..59252912-chr1:59759683..59766457,13	MCF-7	breast:
9	chr1:59249653..59250360-chr11:47869934..47870678,2	Hela-S3	cervix:
10	chr1:59249489..59250361-chr17:56709110..56709614,2	HCT-116	colon:
11	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
12	chr1:45196303..45197166-chr1:59249336..59250143,2	Hela-S3	cervix:
13	chr1:59248023..59251652-chr1:59759822..59764138,5	MCF-7	breast:
14	chr1:59249642..59250559-chr7:151215635..151216340,2	Hela-S3	cervix:
15	chr1:59250077..59250595-chr15:43817366..43818272,2	Hela-S3	cervix:
16	chr1:59248634..59251587-chr1:59519796..59523397,3	K562	blood:
17	chr1:59249398..59250266-chr11:62608563..62609478,2	HCT-116	colon:
18	chr1:59249602..59250123-chr9:34612018..34612614,2	Hela-S3	cervix:
19	chr1:59163564..59170812-chr1:59245390..59251956,13	K562	blood:
20	chr1:59249289..59250803-chr1:59761583..59764317,2	K562	blood:
21	chr1:59244876..59251429-chr1:59540803..59548111,10	K562	blood:
22	chr1:59249627..59250197-chr14:90862800..90863596,2	HCT-116	colon:
23	chr1:59249358..59250200-chr22:43011055..43011957,2	Hela-S3	cervix:
24	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
25	chr1:59229058..59237226-chr1:59244356..59250672,11	MCF-7	breast:
26	chr1:59162606..59168890-chr1:59243728..59252069,16	K562	blood:
27	chr1:59249836..59250523-chr5:137909713..137910517,2	Hela-S3	cervix:
28	chr1:59249984..59250670-chr1:59281053..59281725,3	Hela-S3	cervix:
29	chr1:59154836..59157699-chr1:59248547..59250761,2	MCF-7	breast:
30	chr1:59249789..59250484-chr21:38738324..38739147,2	Hela-S3	cervix:
31	chr1:59248724..59251140-chr1:59611823..59614628,3	MCF-7	breast:
32	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
33	chr1:59243405..59253875-chr1:59275011..59289058,45	MCF-7	breast:

Variant related genes	Relation type
LINC01135	TF binding region
JUN	TF binding region
ENSG00000249962	Chromatin interaction
ENSG00000198668	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000224609	Chromatin interaction
ENSG00000156467	Chromatin interaction
ENSG00000254224	Chromatin interaction
ENSG00000235215	Chromatin interaction
ENSG00000241042	Chromatin interaction
ENSG00000162601	Chromatin interaction
ENSG00000232936	Chromatin interaction
ENSG00000264081	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000164967	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000272226	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000237352	Chromatin interaction
ENSG00000172456	Chromatin interaction
ENSG00000166401	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000154222	Chromatin interaction
ENSG00000106615	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4647000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703586	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs74077862	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7537884	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]

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	esv1798968	chr1:59246581-59251097	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1799803	chr1:59246581-59251097	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv12569	chr1:59247251-59250394	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	52 gene(s)	inside rSNPs	diseases
4	esv1800016	chr1:59247993-59250312	Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
5	esv1801003	chr1:59247993-59250312	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
6	esv1801034	chr1:59247993-59250312	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
7	esv1802607	chr1:59247993-59250312	Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
8	esv1802992	chr1:59247993-59251097	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	esv1800997	chr1:59249031-59250312	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	46 gene(s)	inside rSNPs	diseases
10	esv1793770	chr1:59249263-59250312	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	46 gene(s)	inside rSNPs	diseases
11	esv1801296	chr1:59249263-59250312	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	46 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	chr1:59245200-59251400	Active TSS	Aorta	Aorta
2	chr1:59245600-59250600	Active TSS	HMEC	breast
3	chr1:59245600-59251000	Active TSS	HSMMtube	muscle
4	chr1:59245600-59251400	Active TSS	Psoas Muscle	Psoas
5	chr1:59246000-59251200	Active TSS	Liver	Liver
6	chr1:59246200-59251600	Active TSS	Fetal Kidney	kidney
7	chr1:59246400-59251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:59246600-59251200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:59246600-59251200	Active TSS	A549	lung
10	chr1:59246600-59251400	Active TSS	Ovary	ovary
11	chr1:59246800-59251000	Active TSS	HSMM	muscle
12	chr1:59246800-59251200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:59246800-59251400	Active TSS	Colon Smooth Muscle	Colon
14	chr1:59246800-59252000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:59247000-59251200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:59247000-59251200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:59247000-59251200	Active TSS	Brain Angular Gyrus	brain
18	chr1:59247000-59251200	Active TSS	Brain Anterior Caudate	brain
19	chr1:59247000-59251200	Active TSS	Brain Hippocampus Middle	brain
20	chr1:59247000-59251200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:59247000-59251200	Active TSS	Fetal Heart	heart
22	chr1:59247000-59251200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:59247000-59251400	Active TSS	Brain Substantia Nigra	brain
24	chr1:59247200-59251000	Active TSS	Fetal Lung	lung
25	chr1:59247200-59251000	Active TSS	NH-A	brain
26	chr1:59247200-59251400	Active TSS	Small Intestine	intestine
27	chr1:59247400-59250600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:59247400-59251000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
29	chr1:59247400-59251400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:59247800-59251200	Active TSS	Hela-S3	cervix
31	chr1:59248000-59250800	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:59248000-59251000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:59248000-59251000	Active TSS	Fetal Muscle Leg	muscle
34	chr1:59248000-59251200	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr1:59248000-59251200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:59248000-59251200	Active TSS	Brain Cingulate Gyrus	brain
37	chr1:59248000-59251200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:59248000-59251400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:59248000-59252000	Active TSS	Primary T cells from cord blood	blood
40	chr1:59248200-59250600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
41	chr1:59248200-59251200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:59248400-59251000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:59248400-59251000	Active TSS	Duodenum Mucosa	Duodenum
44	chr1:59248400-59251000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:59248400-59251000	Active TSS	HUVEC	blood vessel
46	chr1:59248400-59251200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:59248400-59251400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr1:59248400-59251600	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:59248400-59251800	Active TSS	Right Ventricle	heart
50	chr1:59248600-59250800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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