Variant report

Variant	rs17265089
Chromosome Location	chr1:59250675-59250676
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	POLR2A	chr1:59244106-59251818	U87	brain:	n/a	n/a
3	POLR2A	chr1:59245147-59251676	Hela-S3	cervix:	n/a	n/a
4	EP300	chr1:59249464-59251275	GM12878	blood:	n/a	chr1:59250255-59250264 chr1:59250260-59250276 chr1:59249576-59249590 chr1:59250316-59250323 chr1:59249489-59249505
5	MAX	chr1:59247473-59251323	GM12878	blood:	n/a	chr1:59249843-59249852
6	POLR2A	chr1:59247151-59251494	GM12892	blood:	n/a	n/a
7	RELA	chr1:59249408-59251774	GM18951	blood:	n/a	n/a
8	POLR2A	chr1:59247671-59250698	H1-hESC	embryonic stem cell:	n/a	n/a
9	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
10	POLR2A	chr1:59243934-59251872	U87	brain:	n/a	n/a
11	CHD1	chr1:59244118-59252745	IMR90	lung:	n/a	chr1:59250203-59250213
12	POLR2A	chr1:59249449-59251289	HCT-116	colon:	n/a	n/a
13	RCOR1	chr1:59248856-59251704	Hela-S3	cervix:	n/a	n/a
14	HEY1	chr1:59246437-59251188	K562	blood:	n/a	chr1:59250260-59250275 chr1:59249195-59249210
15	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
16	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
17	HDAC2	chr1:59250594-59251307	MCF-7	breast:	n/a	chr1:59250779-59250788 chr1:59250783-59250792 chr1:59250785-59250794 chr1:59250781-59250790
18	POLR2A	chr1:59244614-59251725	HUVEC	blood vessel:	n/a	n/a
19	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
20	TCF12	chr1:59248641-59251958	SK-N-SH	brain:	n/a	chr1:59249475-59249485 chr1:59251331-59251338 chr1:59249498-59249508
21	POLR2A	chr1:59247171-59251601	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr1:59250527-59250917	GM12878	blood:	n/a	chr1:59250782-59250791 chr1:59250717-59250731 chr1:59250784-59250793 chr1:59250780-59250789 chr1:59250730-59250743 chr1:59250730-59250743
23	GATA3	chr1:59249234-59251270	A549	lung:	n/a	chr1:59249740-59249752
24	EP300	chr1:59250520-59251034	GM12878	blood:	n/a	n/a
25	MAZ	chr1:59249382-59251156	HepG2	liver:	n/a	chr1:59249843-59249852
26	POLR2A	chr1:59249146-59251081	K562	blood:	n/a	n/a
27	RAD21	chr1:59250644-59251680	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr1:59249412-59251656	MCF10A-Er-Src	breast:	n/a	chr1:59249843-59249852
29	CBX3	chr1:59250597-59251067	K562	blood:	n/a	n/a
30	CREB1	chr1:59250568-59250949	A549	lung:	n/a	n/a
31	EBF1	chr1:59249593-59251721	GM12878	blood:	n/a	chr1:59250361-59250372
32	ELF1	chr1:59250557-59250985	A549	lung:	n/a	chr1:59250728-59250740 chr1:59250821-59250830
33	POLR2A	chr1:59247146-59251217	HepG2	liver:	n/a	n/a
34	RCOR1	chr1:59249425-59251414	K562	blood:	n/a	n/a
35	POU2F2	chr1:59250563-59250975	GM12878	blood:	n/a	n/a
36	ELK1	chr1:59249405-59251092	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:59244523-59251294	SK-N-SH	brain:	n/a	n/a
38	CHD2	chr1:59248766-59251257	GM12878	blood:	n/a	chr1:59250203-59250213
39	CEBPB	chr1:59250253-59251061	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:59247451-59251336	GM12892	blood:	n/a	n/a
41	RAD21	chr1:59247406-59252535	IMR90	lung:	n/a	chr1:59249492-59249505 chr1:59250252-59250265 chr1:59249113-59249126
42	POLR2A	chr1:59247048-59251502	GM12892	blood:	n/a	n/a
43	MAX	chr1:59249147-59251058	K562	blood:	n/a	chr1:59249843-59249852
44	ELK4	chr1:59249581-59251121	Hela-S3	cervix:	n/a	chr1:59250313-59250324
45	CUX1	chr1:59249672-59251013	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr1:59249417-59251167	GM12878	blood:	n/a	n/a
47	GTF2F1	chr1:59249438-59251091	Hela-S3	cervix:	n/a	n/a
48	TCF12	chr1:59249035-59251341	A549	lung:	n/a	chr1:59249475-59249485 chr1:59251331-59251338 chr1:59249498-59249508
49	CCNT2	chr1:59247344-59251139	K562	blood:	n/a	chr1:59251021-59251030 chr1:59251014-59251023 chr1:59249183-59249192
50	HCFC1	chr1:59249452-59251242	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:59250642-59250692	HCT-116	colon:	n/a
2	chr1:59250642-59250692	GM19239	blood:	n/a
3	chr1:59250642-59250692	BJ	skin:	n/a
4	chr1:59250642-59250692	Caco-2	colon:	n/a
5	chr1:59250642-59250692	RPTEC	kidney:	n/a
6	chr1:59250642-59250692	HEK293	kidney:	embryo
7	chr1:59250642-59250692	NH-A	brain:	n/a
8	chr1:59250642-59250692	GM06990	blood:	n/a
9	chr1:59250642-59250692	HIPEpiC	eye:	n/a
10	chr1:59250642-59250692	NB4	blood:	n/a
11	chr1:59250642-59250692	HMEC	breast:	n/a
12	chr1:59250642-59250692	CMK	blood:	n/a
13	chr1:59250642-59250692	HPAEpiC	pulmonary alveolar:	n/a
14	chr1:59250642-59250692	ovcar-3	ovarian:	n/a
15	chr1:59250642-59250692	HepG2	liver:	n/a
16	chr1:59250642-59250692	NT2-D1	testis:	n/a
17	chr1:59250642-59250692	PrEC	prostate:	n/a
18	chr1:59250642-59250692	HRCEpiC	kidney:	n/a
19	chr1:59250642-59250692	HRPEpiC	eye:	n/a
20	chr1:59250642-59250692	AG04449	skin:	fetal
21	chr1:59250642-59250692	AG09309	skin:	n/a
22	chr1:59250642-59250692	HCPEpiC	choroid plexus:	n/a
23	chr1:59250642-59250692	SK-N-SH	brain:	n/a
24	chr1:59250642-59250692	A549	lung:	n/a
25	chr1:59250642-59250692	HNPCEpiC	eye:	n/a
26	chr1:59250642-59250692	Hela-S3	cervix:	n/a
27	chr1:59250642-59250692	GM12878	blood:	n/a
28	chr1:59250642-59250692	SK-N-SH_RA	brain:	n/a
29	chr1:59250642-59250692	HRE	kidney:	n/a
30	chr1:59250642-59250692	IMR90	lung:	fetal
31	chr1:59250642-59250692	NHBE	bronchial:	n/a
32	chr1:59250642-59250692	LNCaP	prostate:	n/a
33	chr1:59250642-59250692	ProgFib	skin:	n/a
34	chr1:59250642-59250692	AoSMC	blood vessel:	n/a
35	chr1:59250642-59250692	BE2_C	brain:	n/a
36	chr1:59250642-59250692	Jurkat	blood:	n/a
37	chr1:59250642-59250692	HUVEC	blood vessel:	n/a
38	chr1:59250642-59250692	SKMC	muscle:	n/a
39	chr1:59250642-59250692	GM12892	blood:	n/a
40	chr1:59250642-59250692	Hepatocyte	liver:	n/a
41	chr1:59250642-59250692	SK-N-MC	brain:	n/a
42	chr1:59250642-59250692	U87	brain:	n/a
43	chr1:59250642-59250692	ECC-1	luminal epithelium:	n/a
44	chr1:59250642-59250692	HAEpiC	amniotic membrane:	n/a
45	chr1:59250642-59250692	K562	blood:	n/a
46	chr1:59250642-59250692	HCM	heart:	n/a
47	chr1:59250642-59250692	AG09319	gingival:	n/a
48	chr1:59250642-59250692	MCF-7	breast:	n/a
49	chr1:59250642-59250692	HL-60	blood:	n/a
50	chr1:59250642-59250692	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:52830101..52832396-chr1:59247801..59250793,2	K562	blood:
2	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
3	chr1:59245578..59252912-chr1:59759683..59766457,13	MCF-7	breast:
4	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
5	chr1:59248023..59251652-chr1:59759822..59764138,5	MCF-7	breast:
6	chr1:59248634..59251587-chr1:59519796..59523397,3	K562	blood:
7	chr1:59163564..59170812-chr1:59245390..59251956,13	K562	blood:
8	chr1:59249289..59250803-chr1:59761583..59764317,2	K562	blood:
9	chr1:59244876..59251429-chr1:59540803..59548111,10	K562	blood:
10	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
11	chr1:59162606..59168890-chr1:59243728..59252069,16	K562	blood:
12	chr1:59154836..59157699-chr1:59248547..59250761,2	MCF-7	breast:
13	chr1:59248724..59251140-chr1:59611823..59614628,3	MCF-7	breast:
14	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
15	chr1:59243405..59253875-chr1:59275011..59289058,45	MCF-7	breast:

Variant related genes	Relation type
LINC01135	TF binding region
JUN	TF binding region
JUN	CpG island
LINC01135	CpG island
ENSG00000154222	Chromatin interaction
ENSG00000241042	Chromatin interaction
ENSG00000172456	Chromatin interaction
ENSG00000235215	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000224609	Chromatin interaction
ENSG00000237352	Chromatin interaction
ENSG00000272226	Chromatin interaction
ENSG00000162601	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10157302	1.00[ASN][1000 genomes]
rs10158603	1.00[ASN][1000 genomes]
rs11688	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807819	1.00[ASN][1000 genomes]
rs12723424	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12752760	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17264985	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1980700	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811890	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33989940	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34328062	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34399110	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34417049	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34451092	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34938302	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34984409	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35299642	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35315513	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35354349	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55805512	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61778520	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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

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	chr1:59245600-59251000	Active TSS	HSMMtube	muscle
3	chr1:59245600-59251400	Active TSS	Psoas Muscle	Psoas
4	chr1:59246000-59251200	Active TSS	Liver	Liver
5	chr1:59246200-59251600	Active TSS	Fetal Kidney	kidney
6	chr1:59246400-59251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:59246600-59251200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:59246600-59251200	Active TSS	A549	lung
9	chr1:59246600-59251400	Active TSS	Ovary	ovary
10	chr1:59246800-59251000	Active TSS	HSMM	muscle
11	chr1:59246800-59251200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:59246800-59251400	Active TSS	Colon Smooth Muscle	Colon
13	chr1:59246800-59252000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:59247000-59251200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:59247000-59251200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:59247000-59251200	Active TSS	Brain Angular Gyrus	brain
17	chr1:59247000-59251200	Active TSS	Brain Anterior Caudate	brain
18	chr1:59247000-59251200	Active TSS	Brain Hippocampus Middle	brain
19	chr1:59247000-59251200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr1:59247000-59251200	Active TSS	Fetal Heart	heart
21	chr1:59247000-59251200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:59247000-59251400	Active TSS	Brain Substantia Nigra	brain
23	chr1:59247200-59251000	Active TSS	Fetal Lung	lung
24	chr1:59247200-59251000	Active TSS	NH-A	brain
25	chr1:59247200-59251400	Active TSS	Small Intestine	intestine
26	chr1:59247400-59251000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr1:59247400-59251400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:59247800-59251200	Active TSS	Hela-S3	cervix
29	chr1:59248000-59250800	Active TSS	Fetal Muscle Trunk	muscle
30	chr1:59248000-59251000	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr1:59248000-59251000	Active TSS	Fetal Muscle Leg	muscle
32	chr1:59248000-59251200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:59248000-59251200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:59248000-59251200	Active TSS	Brain Cingulate Gyrus	brain
35	chr1:59248000-59251200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:59248000-59251400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:59248000-59252000	Active TSS	Primary T cells from cord blood	blood
38	chr1:59248200-59251200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:59248400-59251000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:59248400-59251000	Active TSS	Duodenum Mucosa	Duodenum
41	chr1:59248400-59251000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr1:59248400-59251000	Active TSS	HUVEC	blood vessel
43	chr1:59248400-59251200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:59248400-59251400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:59248400-59251600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:59248400-59251800	Active TSS	Right Ventricle	heart
47	chr1:59248600-59250800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:59248600-59251000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:59248600-59251000	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:59248600-59251000	Active TSS	Adipose Nuclei	Adipose

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