Variant report

Variant	rs73839129
Chromosome Location	chr3:52716380-52716381
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	chr3:52716048-52716437	K562	blood:	n/a	n/a
2	FOS	chr3:52715979-52716409	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr3:52715826-52716438	HepG2	liver:	n/a	n/a
4	CTCF	chr3:52715906-52716530	A549	lung:	n/a	n/a
5	TEAD4	chr3:52715856-52716448	HepG2	liver:	n/a	n/a
6	FOXA1	chr3:52715903-52716391	HepG2	liver:	n/a	n/a
7	STAT3	chr3:52716115-52716392	GM12878	blood:	n/a	chr3:52716124-52716135 chr3:52716126-52716135 chr3:52716336-52716343 chr3:52716123-52716137 chr3:52716125-52716134
8	MXI1	chr3:52715612-52716585	SK-N-SH	brain:	n/a	n/a
9	EP300	chr3:52715971-52716420	HepG2	liver:	n/a	chr3:52716392-52716406 chr3:52716391-52716405
10	MYC	chr3:52715983-52716382	K562	blood:	n/a	n/a
11	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
12	NFIC	chr3:52715896-52716539	GM12878	blood:	n/a	chr3:52716417-52716434 chr3:52716417-52716433
13	MYBL2	chr3:52715827-52716429	HepG2	liver:	n/a	n/a
14	CTCF	chr3:52716055-52716479	K562	blood:	n/a	n/a
15	RAD21	chr3:52716030-52716385	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr3:52716240-52716390	HMEC	breast:	n/a	n/a
17	ZMIZ1	chr3:52716094-52716433	K562	blood:	n/a	n/a
18	MXI1	chr3:52716018-52716464	GM12878	blood:	n/a	n/a
19	CTCF	chr3:52716240-52716390	HCFaa	heart:	n/a	n/a
20	CTCF	chr3:52716240-52716390	HCT-116	colon:	n/a	n/a
21	ZNF384	chr3:52716155-52716519	GM12878	blood:	n/a	n/a
22	MAX	chr3:52715996-52716388	K562	blood:	n/a	n/a
23	RAD21	chr3:52715923-52716446	HepG2	liver:	n/a	n/a
24	CTCF	chr3:52715976-52716514	HCT-116	colon:	n/a	n/a
25	CTCF	chr3:52715934-52716594	SK-N-SH	brain:	n/a	n/a
26	RAD21	chr3:52716033-52716428	HepG2	liver:	n/a	n/a
27	RUNX3	chr3:52715859-52716392	GM12878	blood:	n/a	n/a
28	BHLHE40	chr3:52716036-52716388	HepG2	liver:	n/a	chr3:52716264-52716285
29	RAD21	chr3:52715844-52716595	SK-N-SH	brain:	n/a	n/a
30	MAFK	chr3:52715691-52716475	HepG2	liver:	n/a	chr3:52715808-52715822 chr3:52715807-52715823 chr3:52715805-52715816 chr3:52715804-52715819 chr3:52715805-52715825 chr3:52715809-52715819 chr3:52715803-52715817 chr3:52715804-52715820 chr3:52715809-52715818
31	CTCF	chr3:52715938-52716602	HCT-116	colon:	n/a	n/a
32	USF1	chr3:52716024-52716430	H1-hESC	embryonic stem cell:	n/a	chr3:52716264-52716285
33	RAD21	chr3:52715861-52716474	HCT-116	colon:	n/a	n/a
34	IKZF1	chr3:52715652-52716434	GM12878	blood:	n/a	n/a
35	MAX	chr3:52716069-52716390	NB4	blood:	n/a	n/a
36	MYC	chr3:52716009-52716427	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr3:52716078-52716429	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr3:52716069-52716408	H1-hESC	embryonic stem cell:	n/a	n/a
39	BHLHE40	chr3:52716020-52716407	K562	blood:	n/a	chr3:52716264-52716285
40	CTCF	chr3:52716050-52716395	IMR90	lung:	n/a	n/a
41	RAD21	chr3:52715962-52716411	GM12878	blood:	n/a	n/a
42	CTCF	chr3:52716007-52716424	GM12878	blood:	n/a	n/a
43	CTCF	chr3:52716240-52716390	HCPEpiC	choroid plexus:	n/a	n/a
44	JUND	chr3:52715737-52716405	K562	blood:	n/a	n/a
45	FOS	chr3:52715966-52716383	MCF10A-Er-Src	breast:	n/a	n/a
46	NFIC	chr3:52715865-52716413	GM12878	blood:	n/a	n/a
47	RCOR1	chr3:52716062-52716402	K562	blood:	n/a	n/a
48	ZNF384	chr3:52716048-52716436	K562	blood:	n/a	n/a
49	MYC	chr3:52716057-52716381	H1-hESC	embryonic stem cell:	n/a	n/a
50	MTA3	chr3:52715865-52716406	GM12878	blood:	n/a	n/a

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

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11510435	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.92[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	0.86[AFR][1000 genomes]
rs72950424	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][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	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
4	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52710000-52717200	Strong transcription	Fetal Stomach	stomach
6	chr3:52712600-52719400	Weak transcription	Gastric	stomach
7	chr3:52713200-52719200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:52713600-52716400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:52713600-52718600	Enhancers	Adipose Nuclei	Adipose
10	chr3:52713600-52719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52713800-52718000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52713800-52718400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:52713800-52719200	Weak transcription	Aorta	Aorta
14	chr3:52714000-52718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:52714200-52717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:52714200-52717600	Weak transcription	Lung	lung
17	chr3:52714200-52718000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:52714200-52718400	Weak transcription	Colonic Mucosa	Colon
19	chr3:52714200-52718400	Weak transcription	Stomach Mucosa	stomach
20	chr3:52714200-52718600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:52714200-52718800	Weak transcription	Right Atrium	heart
22	chr3:52714200-52718800	Weak transcription	Right Ventricle	heart
23	chr3:52714200-52719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52714200-52719200	Weak transcription	Esophagus	oesophagus
25	chr3:52714200-52719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:52714400-52717800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:52714400-52718200	Weak transcription	HUVEC	blood vessel
28	chr3:52714400-52718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:52714400-52718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:52714600-52718200	Enhancers	NHLF	lung
31	chr3:52714600-52718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:52714800-52716400	Genic enhancers	Fetal Intestine Large	intestine
33	chr3:52714800-52716600	Weak transcription	Fetal Brain Male	brain
34	chr3:52714800-52716800	Enhancers	Ovary	ovary
35	chr3:52714800-52717600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:52714800-52718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:52714800-52719000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:52715000-52716800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:52715000-52716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:52715000-52716800	Enhancers	Brain Substantia Nigra	brain
41	chr3:52715000-52717400	Weak transcription	Primary B cells from cord blood	blood
42	chr3:52715000-52718000	Enhancers	HepG2	liver
43	chr3:52715200-52716800	Enhancers	Fetal Intestine Small	intestine
44	chr3:52715200-52716800	Flanking Active TSS	GM12878-XiMat	blood
45	chr3:52715200-52718400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:52715200-52719000	Weak transcription	Placenta	Placenta
47	chr3:52715200-52719400	Weak transcription	Spleen	Spleen
48	chr3:52715400-52716800	Enhancers	Brain Hippocampus Middle	brain
49	chr3:52715400-52716800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:52715400-52717000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links