Variant report

Variant	rs72960229
Chromosome Location	chr3:52739890-52739891
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:370)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:370 , 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	IRF1	chr3:52739774-52740212	K562	blood:	n/a	n/a
2	CTCF	chr3:52739800-52739950	AG04449	skin:	n/a	n/a
3	POLR2A	chr3:52739505-52740396	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:52739337-52740585	K562	blood:	n/a	n/a
5	ZMIZ1	chr3:52739470-52740398	K562	blood:	n/a	n/a
6	ZEB1	chr3:52739836-52740277	GM12878	blood:	n/a	n/a
7	HDAC2	chr3:52739603-52740392	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52739403-52740552	GM12891	blood:	n/a	n/a
9	GABPA	chr3:52739557-52740580	A549	lung:	n/a	n/a
10	POLR2A	chr3:52739455-52740697	GM12891	blood:	n/a	n/a
11	POLR2A	chr3:52738427-52740420	HepG2	liver:	n/a	n/a
12	YY1	chr3:52739547-52740480	HepG2	liver:	n/a	n/a
13	MYC	chr3:52739541-52740425	K562	blood:	n/a	n/a
14	REST	chr3:52739789-52740465	A549	lung:	n/a	n/a
15	E2F6	chr3:52739619-52740538	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:52739466-52740688	Hela-S3	cervix:	n/a	n/a
17	PAX5	chr3:52739449-52740497	GM12878	blood:	n/a	n/a
18	CEBPB	chr3:52739648-52740250	Hela-S3	cervix:	n/a	n/a
19	RCOR1	chr3:52739559-52740330	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:52739512-52741064	MCF10A-Er-Src	breast:	n/a	n/a
21	MAZ	chr3:52739589-52740496	Hela-S3	cervix:	n/a	n/a
22	NANOG	chr3:52739509-52740090	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:52739494-52740513	GM18526	blood:	n/a	n/a
24	RCOR1	chr3:52739506-52740375	K562	blood:	n/a	n/a
25	POLR2A	chr3:52739454-52740611	MCF-7	breast:	n/a	n/a
26	RCOR1	chr3:52739416-52740376	HepG2	liver:	n/a	n/a
27	MAX	chr3:52739599-52740356	HUVEC	blood vessel:	n/a	n/a
28	YY1	chr3:52739370-52740681	SK-N-SH	brain:	n/a	n/a
29	HDAC2	chr3:52739778-52740089	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:52738761-52740726	K562	blood:	n/a	n/a
31	YY1	chr3:52739439-52740558	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr3:52739569-52740542	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr3:52739527-52740445	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:52739478-52740379	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr3:52739579-52740355	HepG2	liver:	n/a	n/a
36	MAX	chr3:52739793-52740458	H1-hESC	embryonic stem cell:	n/a	n/a
37	UBTF	chr3:52739568-52740510	K562	blood:	n/a	n/a
38	MAX	chr3:52739341-52740434	NB4	blood:	n/a	n/a
39	ELF1	chr3:52739634-52740413	HepG2	liver:	n/a	n/a
40	YY1	chr3:52739445-52740559	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:52739423-52740430	HCT-116	colon:	n/a	n/a
42	POLR2A	chr3:52739367-52740453	U87	brain:	n/a	n/a
43	POLR2A	chr3:52738437-52740442	HepG2	liver:	n/a	n/a
44	EP300	chr3:52739740-52740319	A549	lung:	n/a	n/a
45	CREB1	chr3:52739792-52740384	K562	blood:	n/a	n/a
46	GABPA	chr3:52739605-52740484	GM12878	blood:	n/a	n/a
47	GABPA	chr3:52739598-52740672	K562	blood:	n/a	n/a
48	ZKSCAN1	chr3:52739532-52740590	Hela-S3	cervix:	n/a	n/a
49	CREB1	chr3:52739514-52740523	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr3:52739397-52740532	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
2	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
3	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
4	chr12:56509849..56510496-chr3:52739808..52740679,2	HCT-116	colon:
5	chr3:52733044..52735275-chr3:52738797..52740602,3	MCF-7	breast:
6	chr12:7052734..7053301-chr3:52739531..52740179,2	Hela-S3	cervix:
7	chr3:52739553..52740477-chr7:135346553..135347414,2	Hela-S3	cervix:
8	chr3:52570222..52571915-chr3:52739151..52740818,2	MCF-7	breast:
9	chr3:52731236..52732930-chr3:52738101..52740472,2	MCF-7	breast:
10	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLT8D1-1	chr3:52739463-52740048	NONHSAT089951

No data

Variant related genes	Relation type
GLT8D1	TF binding region
SPCS1	TF binding region
ENSG00000163938	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000252787	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000243317	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs72947566	0.84[AFR][1000 genomes]
rs72950414	0.84[AFR][1000 genomes]
rs72960204	0.96[AFR][1000 genomes]
rs72960259	0.91[AFR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 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	chr3:52737800-52740800	Active TSS	Ovary	ovary
2	chr3:52737800-52741400	Active TSS	NHLF	lung
3	chr3:52737800-52741600	Active TSS	Colonic Mucosa	Colon
4	chr3:52738000-52741400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:52738000-52741400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:52738000-52741600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:52738200-52740200	Active TSS	HepG2	liver
8	chr3:52738200-52740800	Active TSS	NH-A	brain
9	chr3:52738200-52741400	Active TSS	NHDF-Ad	bronchial
10	chr3:52738200-52741800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:52738400-52740600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:52738400-52741600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:52738400-52741800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:52738600-52741000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52738600-52741200	Active TSS	Small Intestine	intestine
16	chr3:52738600-52741400	Active TSS	Aorta	Aorta
17	chr3:52738800-52741000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr3:52738800-52741200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:52738800-52741200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:52738800-52741200	Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:52738800-52741200	Active TSS	Gastric	stomach
22	chr3:52738800-52741200	Active TSS	Psoas Muscle	Psoas
23	chr3:52738800-52741400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:52738800-52741600	Active TSS	A549	lung
25	chr3:52739000-52740400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:52739000-52740600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:52739000-52740600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52739000-52740600	Active TSS	Fetal Stomach	stomach
29	chr3:52739000-52740600	Active TSS	Placenta Amnion	Placenta Amnion
30	chr3:52739000-52740600	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:52739000-52740800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:52739000-52740800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52739000-52740800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:52739000-52740800	Active TSS	Brain Anterior Caudate	brain
35	chr3:52739000-52740800	Active TSS	Colon Smooth Muscle	Colon
36	chr3:52739000-52740800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:52739000-52740800	Active TSS	Fetal Lung	lung
38	chr3:52739000-52740800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr3:52739000-52740800	Active TSS	HUVEC	blood vessel
40	chr3:52739000-52741000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52739000-52741000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:52739000-52741000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52739000-52741000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:52739000-52741000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:52739000-52741000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52739000-52741000	Active TSS	Fetal Intestine Small	intestine
47	chr3:52739000-52741000	Active TSS	Lung	lung
48	chr3:52739000-52741000	Active TSS	Osteobl	bone
49	chr3:52739000-52741200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:52739000-52741200	Active TSS	Fetal Kidney	kidney

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