Variant report

Variant	rs13407873
Chromosome Location	chr2:64067840-64067841
allele	C/T
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	MYC	chr2:64067811-64068054	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:64067662-64069172	HUVEC	blood vessel:	n/a	n/a
3	SIN3A	chr2:64067241-64069212	GM12878	blood:	n/a	n/a
4	NFATC1	chr2:64067578-64068440	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:64067418-64069792	K562	blood:	n/a	n/a
6	WRNIP1	chr2:64067471-64068343	GM12878	blood:	n/a	n/a
7	TAF1	chr2:64067731-64068211	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:64067196-64069274	HL-60	blood:	n/a	n/a
9	CTCF	chr2:64067720-64067870	GM12864	blood:	n/a	n/a
10	MAX	chr2:64067261-64069107	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP4	chr2:64067437-64069169	H1-hESC	embryonic stem cell:	n/a	chr2:64068388-64068404 chr2:64067994-64068010
12	POLR2A	chr2:64067693-64069196	HepG2	liver:	n/a	n/a
13	MAX	chr2:64067753-64068345	K562	blood:	n/a	n/a
14	POLR2A	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:64067196-64069886	ProgFib	skin:	n/a	n/a
16	CTCF	chr2:64067840-64067990	HMEC	breast:	n/a	n/a
17	PML	chr2:64067648-64068445	MCF-7	breast:	n/a	n/a
18	KAP1	chr2:64067660-64070291	U2OS	brain:	n/a	n/a
19	ZNF143	chr2:64067536-64069084	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP1	chr2:64067715-64068334	HepG2	liver:	n/a	chr2:64067997-64068006 chr2:64067997-64068011 chr2:64067997-64068007 chr2:64067996-64068008 chr2:64068014-64068035 chr2:64067998-64068007 chr2:64067996-64068008 chr2:64067997-64068007 chr2:64067997-64068006
21	CTCF	chr2:64067800-64067950	BJ	skin:	n/a	n/a
22	TAF1	chr2:64067470-64069236	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr2:64067707-64069234	HUVEC	blood vessel:	n/a	n/a
24	NFIC	chr2:64067755-64068293	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:64067017-64069463	HUVEC	blood vessel:	n/a	n/a
26	STAT5A	chr2:64067482-64069174	GM12878	blood:	n/a	chr2:64068607-64068619 chr2:64067694-64067706
27	POLR2A	chr2:64067515-64069485	PFSK-1	brain:	n/a	n/a
28	SP1	chr2:64067751-64068311	GM12878	blood:	n/a	chr2:64067997-64068006 chr2:64067997-64068011 chr2:64067997-64068007 chr2:64067996-64068008 chr2:64068014-64068035 chr2:64067998-64068007 chr2:64067996-64068008 chr2:64067997-64068007 chr2:64067997-64068006
29	RAD21	chr2:64067649-64068337	HepG2	liver:	n/a	n/a
30	MAX	chr2:64067483-64070170	Hela-S3	cervix:	n/a	n/a
31	SP1	chr2:64067473-64068397	H1-hESC	embryonic stem cell:	n/a	chr2:64067997-64068006 chr2:64067997-64068011 chr2:64067997-64068007 chr2:64067996-64068008 chr2:64068014-64068035 chr2:64067998-64068007 chr2:64067996-64068008 chr2:64067997-64068007 chr2:64067997-64068006
32	NRF1	chr2:64067681-64067929	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP2	chr2:64067754-64068341	H1-hESC	embryonic stem cell:	n/a	chr2:64068023-64068033 chr2:64067996-64068011 chr2:64068027-64068050 chr2:64068060-64068083 chr2:64067999-64068008
34	POLR2A	chr2:64067326-64069633	K562	blood:	n/a	n/a
35	MYBL2	chr2:64067599-64070273	HepG2	liver:	n/a	n/a
36	EP300	chr2:64067676-64068308	GM12878	blood:	n/a	chr2:64067764-64067780
37	FOXM1	chr2:64067531-64068328	GM12878	blood:	n/a	n/a
38	TAF1	chr2:64067643-64069065	HepG2	liver:	n/a	n/a
39	IRF3	chr2:64067572-64068235	GM12878	blood:	n/a	chr2:64067994-64068008
40	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
41	POLR2A	chr2:64067434-64069928	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:64067224-64069354	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr2:64067549-64069258	SK-N-SH	brain:	n/a	n/a
44	MAX	chr2:64067522-64069978	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr2:64067485-64069228	GM12891	blood:	n/a	n/a
46	BCL11A	chr2:64067799-64068277	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:64067445-64069126	GM12878	blood:	n/a	n/a
48	HCFC1	chr2:64067197-64069270	Hela-S3	cervix:	n/a	n/a
49	TEAD4	chr2:64067791-64069001	H1-hESC	embryonic stem cell:	n/a	n/a
50	ELF1	chr2:64067431-64069249	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:64067822-64067872	SKMC	muscle:	n/a
2	chr2:64067822-64067872	LNCaP	prostate:	n/a
3	chr2:64067822-64067872	AG09319	gingival:	n/a
4	chr2:64067822-64067872	MCF-7	breast:	n/a
5	chr2:64067822-64067872	ProgFib	skin:	n/a
6	chr2:64067822-64067872	HPAEpiC	pulmonary alveolar:	n/a
7	chr2:64067822-64067872	HCF	heart:	n/a
8	chr2:64067822-64067872	HRCEpiC	kidney:	n/a
9	chr2:64067822-64067872	HUVEC	blood vessel:	n/a
10	chr2:64067822-64067872	RPTEC	kidney:	n/a
11	chr2:64067822-64067872	GM12878	blood:	n/a
12	chr2:64067822-64067872	HAEpiC	amniotic membrane:	n/a
13	chr2:64067822-64067872	AG10803	skin:	n/a
14	chr2:64067822-64067872	Hepatocyte	liver:	n/a
15	chr2:64067822-64067872	HMEC	breast:	n/a
16	chr2:64067822-64067872	SK-N-MC	brain:	n/a
17	chr2:64067822-64067872	HCPEpiC	choroid plexus:	n/a
18	chr2:64067822-64067872	Caco-2	colon:	n/a
19	chr2:64067822-64067872	HNPCEpiC	eye:	n/a
20	chr2:64067822-64067872	NHDF-neo	bronchial:	n/a
21	chr2:64067822-64067872	NB4	blood:	n/a
22	chr2:64067822-64067872	ECC-1	luminal epithelium:	n/a
23	chr2:64067822-64067872	SAEC	small airway:	n/a
24	chr2:64067822-64067872	GM06990	blood:	n/a
25	chr2:64067822-64067872	MCF10A-Er-Src	breast:	n/a
26	chr2:64067822-64067872	NT2-D1	testis:	n/a
27	chr2:64067822-64067872	AoSMC	blood vessel:	n/a
28	chr2:64067822-64067872	BJ	skin:	n/a
29	chr2:64067822-64067872	CMK	blood:	n/a
30	chr2:64067822-64067872	SK-N-SH_RA	brain:	n/a
31	chr2:64067822-64067872	PFSK-1	brain:	n/a
32	chr2:64067822-64067872	HCT-116	colon:	n/a
33	chr2:64067822-64067872	HRE	kidney:	n/a
34	chr2:64067822-64067872	AG04449	skin:	fetal
35	chr2:64067822-64067872	A549	lung:	n/a
36	chr2:64067822-64067872	PrEC	prostate:	n/a
37	chr2:64067822-64067872	HEK293	kidney:	embryo
38	chr2:64067822-64067872	HEEpiC	esophagus:	n/a
39	chr2:64067822-64067872	SK-N-SH	brain:	n/a
40	chr2:64067822-64067872	Hela-S3	cervix:	n/a
41	chr2:64067822-64067872	K562	blood:	n/a
42	chr2:64067822-64067872	IMR90	lung:	fetal
43	chr2:64067822-64067872	ovcar-3	ovarian:	n/a
44	chr2:64067822-64067872	H1-hESC	embryonic stem cell:	embryo
45	chr2:64067822-64067872	GM12892	blood:	n/a
46	chr2:64067822-64067872	Jurkat	blood:	n/a
47	chr2:64067822-64067872	GM19239	blood:	n/a
48	chr2:64067822-64067872	HL-60	blood:	n/a
49	chr2:64067822-64067872	AG09309	skin:	n/a
50	chr2:64067822-64067872	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr19:47551525..47552077-chr2:64067501..64068272,2	NB4	blood:
2	chr2:64067578..64068085-chr6:82461932..82462790,2	NB4	blood:
3	chr2:64067755..64068306-chr6:74230303..74230846,2	NB4	blood:
4	chr2:63816373..63818974-chr2:64066021..64069792,3	MCF-7	breast:
5	chr2:64015153..64018020-chr2:64066514..64068050,2	MCF-7	breast:
6	chr1:28974802..28975912-chr2:64067581..64068743,3	Hela-S3	cervix:
7	chr2:64052299..64060510-chr2:64066102..64071144,11	MCF-7	breast:
8	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
9	chr2:64052304..64056068-chr2:64066396..64069697,6	K562	blood:
10	chr2:32852713..32853638-chr2:64067439..64068207,2	NB4	blood:
11	chr2:64066782..64070718-chr2:64080924..64091365,11	MCF-7	breast:
12	chr2:64065422..64070588-chr2:64080925..64083417,5	K562	blood:
13	chr2:64066677..64069203-chr2:64081708..64084913,3	MCF-7	breast:
14	chr2:64053563..64056956-chr2:64065611..64068830,7	K562	blood:
15	chr2:64053178..64056062-chr2:64067220..64068754,2	MCF-7	breast:
16	chr1:78469811..78470339-chr2:64067570..64068396,2	Hela-S3	cervix:
17	chr17:73084034..73084676-chr2:64067379..64068114,2	Hela-S3	cervix:
18	chr2:63815230..63817166-chr2:64066426..64068247,2	MCF-7	breast:
19	chr17:16341453..16342412-chr2:64067490..64068202,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDPCP-3	chr2:64067177-64067869	NONHSAT071075

Variant related genes	Relation type
UGP2	TF binding region
UGP2	CpG island
ENSG00000018699	Chromatin interaction
ENSG00000130748	Chromatin interaction
ENSG00000170190	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000014641	Chromatin interaction
ENSG00000112773	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000175061	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000143951	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10170601	1.00[AMR][1000 genomes]
rs10175439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10178275	1.00[AMR][1000 genomes]
rs10194235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10194684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10211030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328126	1.00[AMR][1000 genomes]
rs13386582	1.00[AMR][1000 genomes]
rs13387854	1.00[AMR][1000 genomes]
rs13392388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13396651	1.00[AMR][1000 genomes]
rs13405024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13410065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418689	1.00[AMR][1000 genomes]
rs13422518	1.00[AMR][1000 genomes]
rs13424234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13425413	1.00[AMR][1000 genomes]
rs13426789	1.00[AMR][1000 genomes]
rs13427671	1.00[AMR][1000 genomes]
rs13427962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429652	1.00[AMR][1000 genomes]
rs13431016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13431823	1.00[AMR][1000 genomes]
rs9989753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 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	chr2:64065800-64071000	Active TSS	Liver	Liver
2	chr2:64066800-64069800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:64066800-64070600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:64067000-64070000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:64067200-64068000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr2:64067200-64068000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:64067200-64068000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:64067200-64068000	Active TSS	Brain Germinal Matrix	brain
12	chr2:64067200-64069800	Active TSS	Brain Anterior Caudate	brain
13	chr2:64067200-64069800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr2:64067200-64070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:64067200-64070000	Active TSS	Fetal Kidney	kidney
16	chr2:64067200-64070000	Active TSS	Pancreas	Pancrea
17	chr2:64067200-64070000	Active TSS	Rectal Smooth Muscle	rectum
18	chr2:64067200-64070200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:64067200-64070200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr2:64067200-64070200	Active TSS	Gastric	stomach
21	chr2:64067200-64070400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:64067200-64070800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:64067200-64071600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:64067200-64071800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:64067200-64072000	Active TSS	Aorta	Aorta
26	chr2:64067200-64072000	Active TSS	Fetal Muscle Trunk	muscle
27	chr2:64067200-64072200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:64067200-64072200	Active TSS	Colonic Mucosa	Colon
29	chr2:64067200-64072400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:64067200-64073200	Active TSS	Left Ventricle	heart
31	chr2:64067200-64073400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:64067400-64068800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:64067400-64069800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr2:64067400-64070000	Active TSS	GM12878-XiMat	blood
35	chr2:64067400-64070200	Active TSS	Esophagus	oesophagus
36	chr2:64067400-64070200	Active TSS	Lung	lung
37	chr2:64067400-64070200	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr2:64067400-64070400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:64067400-64070400	Active TSS	Ovary	ovary
40	chr2:64067400-64071000	Active TSS	Thymus	Thymus
41	chr2:64067400-64071400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:64067400-64072200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:64067400-64074000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:64067600-64068200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:64067600-64069000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:64067600-64069000	Active TSS	Spleen	Spleen
47	chr2:64067600-64069200	Active TSS	Primary T cells from cord blood	blood
48	chr2:64067600-64069200	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr2:64067600-64069200	Active TSS	Fetal Heart	heart
50	chr2:64067600-64069400	Active TSS	Primary B cells from peripheral blood	blood

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