Variant report

Variant	rs28636773
Chromosome Location	chr3:52444625-52444626
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:388)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:388 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52444560-52444710	HUVEC	blood vessel:	n/a	chr3:52444607-52444623
2	PAX5	chr3:52444508-52444788	GM12878	blood:	n/a	chr3:52444666-52444675
3	SIN3AK20	chr3:52444500-52444978	SK-N-SH	brain:	n/a	n/a
4	EGR1	chr3:52443752-52444980	HCT-116	colon:	n/a	chr3:52443946-52443956 chr3:52444132-52444141 chr3:52444146-52444160 chr3:52444131-52444140
5	CTCF	chr3:52444480-52444630	GM12874	blood:	n/a	chr3:52444607-52444623
6	BHLHE40	chr3:52444528-52445452	GM12878	blood:	n/a	n/a
7	PML	chr3:52444483-52444894	K562	blood:	n/a	n/a
8	ZNF143	chr3:52443982-52444816	H1-hESC	embryonic stem cell:	n/a	chr3:52444026-52444036
9	PML	chr3:52444489-52444802	MCF-7	breast:	n/a	n/a
10	MYC	chr3:52444523-52444713	HepG2	liver:	n/a	n/a
11	E2F4	chr3:52444408-52444779	MCF10A-Er-Src	breast:	n/a	n/a
12	IRF1	chr3:52444562-52445034	K562	blood:	n/a	n/a
13	HCFC1	chr3:52443600-52446586	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:52444581-52444664	GM10266	blood:	n/a	chr3:52444607-52444623
15	CBX3	chr3:52444415-52444806	K562	blood:	n/a	n/a
16	MAX	chr3:52444602-52444866	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:52444516-52444831	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr3:52444600-52444750	AG04450	lung:	n/a	chr3:52444607-52444623
19	RUNX3	chr3:52444425-52445162	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:52443366-52445470	K562	blood:	n/a	n/a
21	JUND	chr3:52443906-52444909	K562	blood:	n/a	n/a
22	POLR2A	chr3:52443756-52444996	GM18951	blood:	n/a	n/a
23	MXI1	chr3:52443508-52445697	IMR90	lung:	n/a	n/a
24	CTCF	chr3:52444515-52444931	GM12878	blood:	n/a	chr3:52444607-52444623 chr3:52444820-52444833
25	POLR2A	chr3:52444510-52445275	GM12891	blood:	n/a	n/a
26	MAX	chr3:52444575-52444796	A549	lung:	n/a	n/a
27	ARID3A	chr3:52444585-52444849	HepG2	liver:	n/a	n/a
28	ZKSCAN1	chr3:52444580-52444899	Hela-S3	cervix:	n/a	n/a
29	MAX	chr3:52444495-52444874	K562	blood:	n/a	n/a
30	TCF7L2	chr3:52444552-52444769	PANC-1	pancreas:	n/a	n/a
31	FOXM1	chr3:52444529-52445071	GM12878	blood:	n/a	n/a
32	TAF1	chr3:52444516-52444848	K562	blood:	n/a	n/a
33	ELK1	chr3:52444621-52444821	K562	blood:	n/a	n/a
34	RUNX3	chr3:52444453-52445071	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52444500-52444928	HepG2	liver:	n/a	n/a
36	SMARCB1	chr3:52444519-52445387	Hela-S3	cervix:	n/a	n/a
37	TCF12	chr3:52444328-52445051	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr3:52444533-52444971	ECC-1	luminal epithelium:	n/a	chr3:52444795-52444809 chr3:52444834-52444843
39	E2F6	chr3:52444502-52444859	K562	blood:	n/a	n/a
40	POLR2A	chr3:52444503-52444884	H1-hESC	embryonic stem cell:	n/a	n/a
41	CREB1	chr3:52443660-52444835	K562	blood:	n/a	n/a
42	CTCF	chr3:52444560-52444710	BJ	skin:	n/a	chr3:52444607-52444623
43	ZNF384	chr3:52444585-52445322	K562	blood:	n/a	n/a
44	STAT1	chr3:52444434-52444665	GM12878	blood:	n/a	n/a
45	CTCF	chr3:52444550-52444674	H1-hESC	embryonic stem cell:	n/a	chr3:52444607-52444623
46	TCF12	chr3:52444551-52444860	GM12878	blood:	n/a	n/a
47	MXI1	chr3:52444540-52444896	K562	blood:	n/a	n/a
48	CTCF	chr3:52444580-52444730	GM12869	blood:	n/a	chr3:52444607-52444623
49	POLR2A	chr3:52444222-52445008	K562	blood:	n/a	n/a
50	YY1	chr3:52444508-52444922	GM12878	blood:	n/a	chr3:52444795-52444809 chr3:52444834-52444843

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52444617-52444667	Hepatocyte	liver:	n/a
2	chr3:52444617-52444667	GM12892	blood:	n/a
3	chr3:52444617-52444667	AG09309	skin:	n/a
4	chr3:52444617-52444667	NHBE	bronchial:	n/a
5	chr3:52444617-52444667	K562	blood:	n/a
6	chr3:52444617-52444667	BE2_C	brain:	n/a
7	chr3:52444617-52444667	AG10803	skin:	n/a
8	chr3:52444617-52444667	HNPCEpiC	eye:	n/a
9	chr3:52444617-52444667	HRCEpiC	kidney:	n/a
10	chr3:52444617-52444667	HMEC	breast:	n/a
11	chr3:52444617-52444667	Jurkat	blood:	n/a
12	chr3:52444617-52444667	IMR90	lung:	fetal
13	chr3:52444617-52444667	HepG2	liver:	n/a
14	chr3:52444617-52444667	SK-N-MC	brain:	n/a
15	chr3:52444617-52444667	U87	brain:	n/a
16	chr3:52444617-52444667	HAEpiC	amniotic membrane:	n/a
17	chr3:52444617-52444667	AG04449	skin:	fetal
18	chr3:52444617-52444667	NH-A	brain:	n/a
19	chr3:52444617-52444667	PrEC	prostate:	n/a
20	chr3:52444617-52444667	SK-N-SH	brain:	n/a
21	chr3:52444617-52444667	LNCaP	prostate:	n/a
22	chr3:52444617-52444667	Hela-S3	cervix:	n/a
23	chr3:52444617-52444667	ProgFib	skin:	n/a
24	chr3:52444617-52444667	GM12891	blood:	n/a
25	chr3:52444617-52444667	GM06990	blood:	n/a
26	chr3:52444617-52444667	ECC-1	luminal epithelium:	n/a
27	chr3:52444617-52444667	HL-60	blood:	n/a
28	chr3:52444617-52444667	A549	lung:	n/a
29	chr3:52444617-52444667	SK-N-SH_RA	brain:	n/a
30	chr3:52444617-52444667	MCF-7	breast:	n/a
31	chr3:52444617-52444667	AoSMC	blood vessel:	n/a
32	chr3:52444617-52444667	AG04450	lung:	fetal
33	chr3:52444617-52444667	HCM	heart:	n/a
34	chr3:52444617-52444667	NB4	blood:	n/a
35	chr3:52444617-52444667	NHDF-neo	bronchial:	n/a
36	chr3:52444617-52444667	HEK293	kidney:	embryo
37	chr3:52444617-52444667	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:52444617-52444667	PFSK-1	brain:	n/a
39	chr3:52444617-52444667	NT2-D1	testis:	n/a
40	chr3:52444617-52444667	HIPEpiC	eye:	n/a
41	chr3:52444617-52444667	HEEpiC	esophagus:	n/a
42	chr3:52444617-52444667	RPTEC	kidney:	n/a
43	chr3:52444617-52444667	HUVEC	blood vessel:	n/a
44	chr3:52444617-52444667	MCF10A-Er-Src	breast:	n/a
45	chr3:52444617-52444667	ovcar-3	ovarian:	n/a
46	chr3:52444617-52444667	GM12878	blood:	n/a
47	chr3:52444617-52444667	SKMC	muscle:	n/a
48	chr3:52444617-52444667	GM19239	blood:	n/a
49	chr3:52444617-52444667	HCF	heart:	n/a
50	chr3:52444617-52444667	Caco-2	colon:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
2	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
3	chr3:52442610..52445343-chr3:52803282..52805357,2	K562	blood:
4	chr13:103425713..103426315-chr3:52444087..52445047,2	NB4	blood:
5	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
6	chr3:52311359..52313564-chr3:52443173..52445594,2	MCF-7	breast:
7	chr3:52015943..52018006-chr3:52443224..52445803,2	K562	blood:
8	chr11:65627121..65628034-chr3:52443935..52444794,2	Hela-S3	cervix:
9	chr3:52271478..52274801-chr3:52443057..52446273,4	K562	blood:
10	chr3:52442891..52445847-chr3:52570573..52572369,2	K562	blood:
11	chr3:52444497..52446102-chr3:52488760..52490756,2	K562	blood:
12	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
13	chr3:52443115..52446014-chr3:52718098..52719635,2	K562	blood:

No data

Variant related genes	Relation type
BAP1	TF binding region
PHF7	TF binding region
PHF7	CpG island
BAP1	CpG island
ENSG00000239732	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000151287	Chromatin interaction
ENSG00000243224	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[EUR][1000 genomes]
rs17052143	1.00[EUR][1000 genomes]
rs28413740	1.00[EUR][1000 genomes]
rs28434358	1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs72947594	1.00[AMR][1000 genomes]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[EUR][1000 genomes]
rs9813489	1.00[EUR][1000 genomes]
rs9813653	1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9821916	1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	1.00[EUR][1000 genomes]
rs9831689	1.00[EUR][1000 genomes]
rs9834363	1.00[EUR][1000 genomes]
rs9834919	1.00[EUR][1000 genomes]
rs9836166	1.00[EUR][1000 genomes]
rs9842960	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9843055	1.00[EUR][1000 genomes]
rs9844178	1.00[EUR][1000 genomes]
rs9845752	1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9864989	1.00[EUR][1000 genomes]
rs9868332	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv3325653	chr3:52442937-52445885	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3354699	chr3:52443212-52445760	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3407957	chr3:52443512-52445260	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr3:52442400-52445200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:52442600-52445800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:52442800-52445200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:52442800-52446400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:52443000-52445600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:52443200-52445000	Active TSS	Placenta Amnion	Placenta Amnion
7	chr3:52443200-52445200	Active TSS	A549	lung
8	chr3:52443200-52445400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52443200-52445600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:52443200-52445600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:52443200-52445600	Active TSS	Gastric	stomach
12	chr3:52443200-52445800	Active TSS	Ovary	ovary
13	chr3:52443200-52446200	Active TSS	K562	blood
14	chr3:52443400-52445000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:52443400-52445000	Active TSS	Fetal Lung	lung
16	chr3:52443400-52445000	Active TSS	NHEK	skin
17	chr3:52443400-52445000	Active TSS	NHLF	lung
18	chr3:52443400-52445200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52443400-52445200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:52443400-52445200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:52443400-52445200	Active TSS	GM12878-XiMat	blood
22	chr3:52443400-52445200	Active TSS	HSMM	muscle
23	chr3:52443400-52445400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:52443400-52445400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52443400-52445400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:52443400-52445400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:52443400-52445400	Active TSS	Small Intestine	intestine
28	chr3:52443400-52445600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:52443400-52445600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:52443400-52445600	Active TSS	Fetal Kidney	kidney
31	chr3:52443400-52445600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:52443400-52445600	Active TSS	Lung	lung
33	chr3:52443400-52445600	Active TSS	Right Atrium	heart
34	chr3:52443400-52445800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:52443400-52445800	Active TSS	NHDF-Ad	bronchial
36	chr3:52443400-52446200	Active TSS	Fetal Intestine Large	intestine
37	chr3:52443400-52446800	Active TSS	Psoas Muscle	Psoas
38	chr3:52443600-52444800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:52443600-52445000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:52443600-52445000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52443600-52445000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:52443600-52445000	Active TSS	Primary T cells from cord blood	blood
43	chr3:52443600-52445000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr3:52443600-52445000	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:52443600-52445000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52443600-52445000	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:52443600-52445000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52443600-52445000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
49	chr3:52443600-52445000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52443600-52445000	Active TSS	Fetal Muscle Leg	muscle

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