Variant report

Variant	rs9836894
Chromosome Location	chr3:52716125-52716126
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	CTCF	chr3:52716060-52716210	A549	lung:	n/a	n/a
2	MXI1	chr3:52715962-52716365	HepG2	liver:	n/a	n/a
3	CTCF	chr3:52716120-52716270	BJ	skin:	n/a	n/a
4	CTCF	chr3:52716100-52716250	HepG2	liver:	n/a	n/a
5	FOS	chr3:52715927-52716351	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr3:52716080-52716230	HPF	lung:	n/a	n/a
7	MYC	chr3:52716048-52716437	K562	blood:	n/a	n/a
8	FOS	chr3:52715979-52716409	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr3:52715826-52716438	HepG2	liver:	n/a	n/a
10	CTCF	chr3:52715906-52716530	A549	lung:	n/a	n/a
11	RAD21	chr3:52716053-52716326	GM12878	blood:	n/a	n/a
12	USF2	chr3:52716096-52716341	HepG2	liver:	n/a	chr3:52716223-52716234 chr3:52716264-52716285 chr3:52716269-52716280
13	HNF4A	chr3:52716015-52716345	HepG2	liver:	n/a	chr3:52716170-52716183 chr3:52716168-52716183 chr3:52716170-52716182 chr3:52716169-52716182 chr3:52716170-52716182 chr3:52716169-52716182
14	CTCF	chr3:52716120-52716270	BE2_C	brain:	n/a	n/a
15	TEAD4	chr3:52715856-52716448	HepG2	liver:	n/a	n/a
16	CTCF	chr3:52716120-52716270	GM12872	blood:	n/a	n/a
17	STAT3	chr3:52715873-52716308	MCF10A-Er-Src	breast:	n/a	chr3:52716124-52716135 chr3:52716126-52716135 chr3:52716123-52716137 chr3:52716125-52716134
18	FOXA1	chr3:52715903-52716391	HepG2	liver:	n/a	n/a
19	CHD1	chr3:52716116-52716357	GM12878	blood:	n/a	n/a
20	STAT3	chr3:52716115-52716392	GM12878	blood:	n/a	chr3:52716124-52716135 chr3:52716126-52716135 chr3:52716336-52716343 chr3:52716123-52716137 chr3:52716125-52716134
21	MAFK	chr3:52715683-52716157	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
22	MXI1	chr3:52715612-52716585	SK-N-SH	brain:	n/a	n/a
23	EP300	chr3:52715971-52716420	HepG2	liver:	n/a	chr3:52716392-52716406 chr3:52716391-52716405
24	MYC	chr3:52715983-52716382	K562	blood:	n/a	n/a
25	RAD21	chr3:52716000-52716346	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:52716060-52716210	GM12871	blood:	n/a	n/a
27	YY1	chr3:52715924-52716327	GM12878	blood:	n/a	n/a
28	CTCF	chr3:52716120-52716270	AG04449	skin:	n/a	n/a
29	MAX	chr3:52716097-52716352	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAZ	chr3:52716106-52716309	GM12878	blood:	n/a	n/a
31	YY1	chr3:52716048-52716331	GM12892	blood:	n/a	n/a
32	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
33	NFIC	chr3:52715896-52716539	GM12878	blood:	n/a	chr3:52716417-52716434 chr3:52716417-52716433
34	MYBL2	chr3:52715827-52716429	HepG2	liver:	n/a	n/a
35	SMC3	chr3:52716080-52716337	K562	blood:	n/a	n/a
36	CTCF	chr3:52716055-52716479	K562	blood:	n/a	n/a
37	RUNX3	chr3:52715904-52716343	GM12878	blood:	n/a	n/a
38	USF1	chr3:52716043-52716345	K562	blood:	n/a	chr3:52716264-52716285
39	CTCF	chr3:52716100-52716250	SAEC	small airway:	n/a	n/a
40	RAD21	chr3:52716030-52716385	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr3:52716080-52716230	GM12864	blood:	n/a	n/a
42	CTCF	chr3:52716100-52716250	A549	lung:	n/a	n/a
43	RAD21	chr3:52716101-52716336	A549	lung:	n/a	n/a
44	USF2	chr3:52716097-52716340	GM12878	blood:	n/a	chr3:52716223-52716234 chr3:52716269-52716280 chr3:52716264-52716285
45	CTCF	chr3:52716120-52716270	GM12870	blood:	n/a	n/a
46	SIN3AK20	chr3:52716060-52716309	PFSK-1	brain:	n/a	n/a
47	PML	chr3:52715979-52716215	GM12878	blood:	n/a	n/a
48	ZMIZ1	chr3:52716094-52716433	K562	blood:	n/a	n/a
49	MXI1	chr3:52716018-52716464	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:52716009-52716278	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
GNL3	TF binding region
PBRM1	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000163938	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13325325	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17052143	1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs35394357	0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6790314	1.00[MEX][hapmap]
rs9814016	1.00[EUR][1000 genomes]
rs9814833	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9834919	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9864989	0.83[AFR][1000 genomes];1.00[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	chr3:52681200-52716200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:52706000-52716200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:52706000-52716200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:52710000-52717200	Strong transcription	Fetal Stomach	stomach
9	chr3:52712600-52719400	Weak transcription	Gastric	stomach
10	chr3:52713200-52719200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:52713600-52716400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:52713600-52718600	Enhancers	Adipose Nuclei	Adipose
13	chr3:52713600-52719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:52713800-52718000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52713800-52718400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:52713800-52719200	Weak transcription	Aorta	Aorta
17	chr3:52714000-52718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:52714200-52717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:52714200-52717600	Weak transcription	Lung	lung
20	chr3:52714200-52718000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:52714200-52718400	Weak transcription	Colonic Mucosa	Colon
22	chr3:52714200-52718400	Weak transcription	Stomach Mucosa	stomach
23	chr3:52714200-52718600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:52714200-52718800	Weak transcription	Right Atrium	heart
25	chr3:52714200-52718800	Weak transcription	Right Ventricle	heart
26	chr3:52714200-52719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:52714200-52719200	Weak transcription	Esophagus	oesophagus
28	chr3:52714200-52719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:52714400-52717800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52714400-52718200	Weak transcription	HUVEC	blood vessel
31	chr3:52714400-52718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:52714400-52718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:52714600-52716200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:52714600-52718200	Enhancers	NHLF	lung
35	chr3:52714600-52718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:52714800-52716400	Genic enhancers	Fetal Intestine Large	intestine
37	chr3:52714800-52716600	Weak transcription	Fetal Brain Male	brain
38	chr3:52714800-52716800	Enhancers	Ovary	ovary
39	chr3:52714800-52717600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:52714800-52718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:52714800-52719000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:52715000-52716800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:52715000-52716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:52715000-52716800	Enhancers	Brain Substantia Nigra	brain
45	chr3:52715000-52717400	Weak transcription	Primary B cells from cord blood	blood
46	chr3:52715000-52718000	Enhancers	HepG2	liver
47	chr3:52715200-52716200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr3:52715200-52716800	Enhancers	Fetal Intestine Small	intestine
49	chr3:52715200-52716800	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:52715200-52718400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links