Variant report

Variant	rs72960204
Chromosome Location	chr3:52716522-52716523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52715906-52716530	A549	lung:	n/a	n/a
2	MXI1	chr3:52715612-52716585	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr3:52716036-52716565	MCF10A-Er-Src	breast:	n/a	chr3:52716124-52716135 chr3:52716126-52716135 chr3:52716336-52716343 chr3:52716123-52716137 chr3:52716125-52716134
4	NFIC	chr3:52715896-52716539	GM12878	blood:	n/a	chr3:52716417-52716434 chr3:52716417-52716433
5	CTCF	chr3:52715934-52716594	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr3:52715844-52716595	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr3:52715938-52716602	HCT-116	colon:	n/a	n/a
8	MXI1	chr3:52715532-52716615	IMR90	lung:	n/a	n/a
9	RAD21	chr3:52715818-52716555	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52716501-52716551	NH-A	brain:	n/a
2	chr3:52716501-52716551	SAEC	small airway:	n/a
3	chr3:52716501-52716551	PrEC	prostate:	n/a
4	chr3:52716501-52716551	PANC-1	pancreas:	n/a
5	chr3:52716501-52716551	HepG2	liver:	n/a
6	chr3:52716501-52716551	SKMC	muscle:	n/a
7	chr3:52716501-52716551	HNPCEpiC	eye:	n/a
8	chr3:52716501-52716551	HUVEC	blood vessel:	n/a
9	chr3:52716501-52716551	HCF	heart:	n/a
10	chr3:52716501-52716551	GM12878	blood:	n/a
11	chr3:52716501-52716551	SK-N-SH	brain:	n/a
12	chr3:52716501-52716551	Jurkat	blood:	n/a
13	chr3:52716501-52716551	NB4	blood:	n/a
14	chr3:52716501-52716551	K562	blood:	n/a
15	chr3:52716501-52716551	NT2-D1	testis:	n/a
16	chr3:52716501-52716551	HRCEpiC	kidney:	n/a
17	chr3:52716501-52716551	AoSMC	blood vessel:	n/a
18	chr3:52716501-52716551	AG04449	skin:	fetal
19	chr3:52716501-52716551	GM12891	blood:	n/a
20	chr3:52716501-52716551	GM06990	blood:	n/a
21	chr3:52716501-52716551	AG10803	skin:	n/a
22	chr3:52716501-52716551	AG09319	gingival:	n/a
23	chr3:52716501-52716551	HRE	kidney:	n/a
24	chr3:52716501-52716551	A549	lung:	n/a
25	chr3:52716501-52716551	Caco-2	colon:	n/a
26	chr3:52716501-52716551	T-47D	breast:	n/a
27	chr3:52716501-52716551	ovcar-3	ovarian:	n/a
28	chr3:52716501-52716551	MCF10A-Er-Src	breast:	n/a
29	chr3:52716501-52716551	PFSK-1	brain:	n/a
30	chr3:52716501-52716551	GM12892	blood:	n/a
31	chr3:52716501-52716551	AG04450	lung:	fetal
32	chr3:52716501-52716551	U87	brain:	n/a
33	chr3:52716501-52716551	HRPEpiC	eye:	n/a
34	chr3:52716501-52716551	NHBE	bronchial:	n/a
35	chr3:52716501-52716551	ECC-1	luminal epithelium:	n/a
36	chr3:52716501-52716551	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:52716501-52716551	H1-hESC	embryonic stem cell:	embryo
38	chr3:52716501-52716551	NHDF-neo	bronchial:	n/a
39	chr3:52716501-52716551	BJ	skin:	n/a
40	chr3:52716501-52716551	RPTEC	kidney:	n/a
41	chr3:52716501-52716551	HEEpiC	esophagus:	n/a
42	chr3:52716501-52716551	LNCaP	prostate:	n/a
43	chr3:52716501-52716551	HIPEpiC	eye:	n/a
44	chr3:52716501-52716551	HCT-116	colon:	n/a
45	chr3:52716501-52716551	ProgFib	skin:	n/a
46	chr3:52716501-52716551	HL-60	blood:	n/a
47	chr3:52716501-52716551	Hela-S3	cervix:	n/a
48	chr3:52716501-52716551	Hepatocyte	liver:	n/a
49	chr3:52716501-52716551	AG09309	skin:	n/a
50	chr3:52716501-52716551	IMR90	lung:	fetal

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52715353..52718281-chr3:52718433..52721429,4	MCF-7	breast:
2	chr3:52707546..52709318-chr3:52716439..52718303,2	K562	blood:
3	chr3:52713114..52715423-chr3:52715774..52718062,2	MCF-7	breast:
4	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
5	chr3:52712073..52717938-chr3:52718038..52722104,14	K562	blood:
6	chr3:52701409..52703551-chr3:52716024..52719023,2	MCF-7	breast:

No data

Variant related genes	Relation type
PBRM1	TF binding region
GNL3	TF binding region
GNL3	CpG island
PBRM1	CpG island
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000168268	Chromatin interaction

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

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

rs_ID	r²[population]
rs12106887	0.82[AFR][1000 genomes]
rs57458352	0.82[AFR][1000 genomes]
rs72947566	0.81[AFR][1000 genomes]
rs72950414	0.87[AFR][1000 genomes]
rs72960229	0.96[AFR][1000 genomes]
rs72960259	0.95[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	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52710000-52717200	Strong transcription	Fetal Stomach	stomach
5	chr3:52712600-52719400	Weak transcription	Gastric	stomach
6	chr3:52713200-52719200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:52713600-52718600	Enhancers	Adipose Nuclei	Adipose
8	chr3:52713600-52719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52713800-52718000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:52713800-52718400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:52713800-52719200	Weak transcription	Aorta	Aorta
12	chr3:52714000-52718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:52714200-52717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:52714200-52717600	Weak transcription	Lung	lung
15	chr3:52714200-52718000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:52714200-52718400	Weak transcription	Colonic Mucosa	Colon
17	chr3:52714200-52718400	Weak transcription	Stomach Mucosa	stomach
18	chr3:52714200-52718600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:52714200-52718800	Weak transcription	Right Atrium	heart
20	chr3:52714200-52718800	Weak transcription	Right Ventricle	heart
21	chr3:52714200-52719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:52714200-52719200	Weak transcription	Esophagus	oesophagus
23	chr3:52714200-52719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:52714400-52717800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:52714400-52718200	Weak transcription	HUVEC	blood vessel
26	chr3:52714400-52718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:52714400-52718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:52714600-52718200	Enhancers	NHLF	lung
29	chr3:52714600-52718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:52714800-52716600	Weak transcription	Fetal Brain Male	brain
31	chr3:52714800-52716800	Enhancers	Ovary	ovary
32	chr3:52714800-52717600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:52714800-52718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:52714800-52719000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:52715000-52716800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:52715000-52716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:52715000-52716800	Enhancers	Brain Substantia Nigra	brain
38	chr3:52715000-52717400	Weak transcription	Primary B cells from cord blood	blood
39	chr3:52715000-52718000	Enhancers	HepG2	liver
40	chr3:52715200-52716800	Enhancers	Fetal Intestine Small	intestine
41	chr3:52715200-52716800	Flanking Active TSS	GM12878-XiMat	blood
42	chr3:52715200-52718400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52715200-52719000	Weak transcription	Placenta	Placenta
44	chr3:52715200-52719400	Weak transcription	Spleen	Spleen
45	chr3:52715400-52716800	Enhancers	Brain Hippocampus Middle	brain
46	chr3:52715400-52716800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:52715400-52717000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:52715400-52717800	Genic enhancers	Dnd41	blood
49	chr3:52715400-52718600	Weak transcription	Psoas Muscle	Psoas
50	chr3:52715600-52716800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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