Variant report

Variant	rs4293553
Chromosome Location	chr2:64067708-64067709
allele	A/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	POLR2A	chr2:64067662-64069172	HUVEC	blood vessel:	n/a	n/a
2	SIN3A	chr2:64067241-64069212	GM12878	blood:	n/a	n/a
3	NFATC1	chr2:64067578-64068440	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:64067418-64069792	K562	blood:	n/a	n/a
5	WRNIP1	chr2:64067471-64068343	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:64067196-64069274	HL-60	blood:	n/a	n/a
7	MAX	chr2:64067261-64069107	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP4	chr2:64067437-64069169	H1-hESC	embryonic stem cell:	n/a	chr2:64068388-64068404 chr2:64067994-64068010
9	POLR2A	chr2:64067693-64069196	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:64067196-64069886	ProgFib	skin:	n/a	n/a
12	PML	chr2:64067648-64068445	MCF-7	breast:	n/a	n/a
13	KAP1	chr2:64067660-64070291	U2OS	brain:	n/a	n/a
14	ZNF143	chr2:64067536-64069084	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr2:64067470-64069236	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr2:64067707-64069234	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr2:64067017-64069463	HUVEC	blood vessel:	n/a	n/a
18	STAT5A	chr2:64067482-64069174	GM12878	blood:	n/a	chr2:64068607-64068619 chr2:64067694-64067706
19	POLR2A	chr2:64067515-64069485	PFSK-1	brain:	n/a	n/a
20	RAD21	chr2:64067649-64068337	HepG2	liver:	n/a	n/a
21	MAX	chr2:64067483-64070170	Hela-S3	cervix:	n/a	n/a
22	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
23	NRF1	chr2:64067681-64067929	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr2:64067326-64069633	K562	blood:	n/a	n/a
25	MYBL2	chr2:64067599-64070273	HepG2	liver:	n/a	n/a
26	EP300	chr2:64067676-64068308	GM12878	blood:	n/a	chr2:64067764-64067780
27	FOXM1	chr2:64067531-64068328	GM12878	blood:	n/a	n/a
28	TAF1	chr2:64067643-64069065	HepG2	liver:	n/a	n/a
29	IRF3	chr2:64067572-64068235	GM12878	blood:	n/a	chr2:64067994-64068008
30	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
31	POLR2A	chr2:64067434-64069928	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr2:64067224-64069354	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr2:64067549-64069258	SK-N-SH	brain:	n/a	n/a
34	MAX	chr2:64067522-64069978	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr2:64067485-64069228	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:64067445-64069126	GM12878	blood:	n/a	n/a
37	HCFC1	chr2:64067197-64069270	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr2:64067431-64069249	MCF-7	breast:	n/a	n/a
39	REST	chr2:64067437-64069483	H1-neurons	neurons:	n/a	chr2:64068680-64068690
40	EP300	chr2:64067676-64068274	GM12878	blood:	n/a	chr2:64067764-64067780
41	RCOR1	chr2:64067595-64068358	K562	blood:	n/a	n/a
42	SIN3AK20	chr2:64067343-64070208	MCF-7	breast:	n/a	n/a
43	POLR2A	chr2:64067379-64069892	PBDE	blood:	n/a	n/a
44	CHD2	chr2:64067446-64069102	GM12878	blood:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
45	RELA	chr2:64067362-64069145	GM15510	blood:	n/a	n/a
46	POLR2A	chr2:64067303-64069117	GM12878	blood:	n/a	n/a
47	BCL3	chr2:64067664-64068604	A549	lung:	n/a	chr2:64068494-64068507
48	SP2	chr2:64067577-64068473	HepG2	liver:	n/a	chr2:64068023-64068033 chr2:64067996-64068011 chr2:64068027-64068050 chr2:64068060-64068083 chr2:64067999-64068008
49	POLR2A	chr2:64067284-64069244	ECC-1	luminal epithelium:	n/a	n/a
50	PML	chr2:64067522-64069860	K562	blood:	n/a	n/a

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	chr2:63816373..63818974-chr2:64066021..64069792,3	MCF-7	breast:
4	chr2:64015153..64018020-chr2:64066514..64068050,2	MCF-7	breast:
5	chr1:28974802..28975912-chr2:64067581..64068743,3	Hela-S3	cervix:
6	chr2:64052299..64060510-chr2:64066102..64071144,11	MCF-7	breast:
7	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
8	chr2:64052304..64056068-chr2:64066396..64069697,6	K562	blood:
9	chr2:32852713..32853638-chr2:64067439..64068207,2	NB4	blood:
10	chr2:64066782..64070718-chr2:64080924..64091365,11	MCF-7	breast:
11	chr2:64065422..64070588-chr2:64080925..64083417,5	K562	blood:
12	chr2:64066677..64069203-chr2:64081708..64084913,3	MCF-7	breast:
13	chr2:64053563..64056956-chr2:64065611..64068830,7	K562	blood:
14	chr2:64053178..64056062-chr2:64067220..64068754,2	MCF-7	breast:
15	chr1:78469811..78470339-chr2:64067570..64068396,2	Hela-S3	cervix:
16	chr2:64023510..64026519-chr2:64063449..64067726,4	K562	blood:
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
ENSG00000143951	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000130748	Chromatin interaction
ENSG00000014641	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000170190	Chromatin interaction
ENSG00000112773	Chromatin interaction
ENSG00000175061	Chromatin interaction
ENSG00000018699	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10201844	0.89[ASW][hapmap]
rs12612549	1.00[ASW][hapmap]
rs4072113	1.00[ASW][hapmap]
rs6546038	1.00[ASW][hapmap]
rs6546039	1.00[ASW][hapmap]
rs6546046	0.81[MKK][hapmap]

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	chr2:64067000-64067800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:64067000-64067800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr2:64067000-64067800	Flanking Active TSS	NH-A	brain
7	chr2:64067000-64070000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:64067200-64067800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:64067200-64067800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:64067200-64067800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:64067200-64067800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:64067200-64067800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr2:64067200-64067800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr2:64067200-64067800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr2:64067200-64067800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr2:64067200-64067800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr2:64067200-64067800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr2:64067200-64067800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:64067200-64067800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:64067200-64067800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:64067200-64067800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:64067200-64067800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:64067200-64067800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:64067200-64067800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr2:64067200-64067800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:64067200-64067800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr2:64067200-64067800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr2:64067200-64067800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:64067200-64067800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr2:64067200-64067800	Flanking Active TSS	Hela-S3	cervix
34	chr2:64067200-64067800	Flanking Active TSS	HMEC	breast
35	chr2:64067200-64067800	Flanking Active TSS	HSMM	muscle
36	chr2:64067200-64067800	Flanking Active TSS	HUVEC	blood vessel
37	chr2:64067200-64067800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:64067200-64067800	Flanking Active TSS	NHEK	skin
39	chr2:64067200-64068000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:64067200-64068000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:64067200-64068000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:64067200-64068000	Active TSS	Brain Germinal Matrix	brain
43	chr2:64067200-64069800	Active TSS	Brain Anterior Caudate	brain
44	chr2:64067200-64069800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr2:64067200-64070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:64067200-64070000	Active TSS	Fetal Kidney	kidney
47	chr2:64067200-64070000	Active TSS	Pancreas	Pancrea
48	chr2:64067200-64070000	Active TSS	Rectal Smooth Muscle	rectum
49	chr2:64067200-64070200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:64067200-64070200	Active TSS	Duodenum Smooth Muscle	Duodenum

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