Variant report

Variant	rs59260394
Chromosome Location	chr6:142619391-142619392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:142619005-142619754	HepG2	liver:	n/a	n/a
2	FOXA2	chr6:142619102-142619541	A549	lung:	n/a	n/a
3	JUN	chr6:142619086-142619898	HepG2	liver:	n/a	n/a
4	EP300	chr6:142618931-142619644	A549	lung:	n/a	n/a
5	STAT3	chr6:142619240-142619421	MCF10A-Er-Src	breast:	n/a	n/a
6	HDAC2	chr6:142618966-142619723	HepG2	liver:	n/a	n/a
7	FOSL2	chr6:142619097-142619637	A549	lung:	n/a	n/a
8	SIN3AK20	chr6:142619178-142619553	A549	lung:	n/a	n/a
9	USF2	chr6:142619206-142619579	HepG2	liver:	n/a	n/a
10	USF1	chr6:142619225-142619548	A549	lung:	n/a	chr6:142619402-142619413
11	SMC3	chr6:142619118-142619696	HepG2	liver:	n/a	n/a
12	FOS	chr6:142619213-142619911	HUVEC	blood vessel:	n/a	n/a
13	REST	chr6:142619189-142620013	H1-neurons	neurons:	n/a	n/a
14	EP300	chr6:142619293-142619754	SK-N-SH_RA	brain:	n/a	n/a
15	TCF12	chr6:142618996-142620165	SK-N-SH	brain:	n/a	n/a
16	TCF12	chr6:142618933-142619792	A549	lung:	n/a	n/a
17	SP1	chr6:142619052-142619603	A549	lung:	n/a	n/a
18	TCF7L2	chr6:142617505-142619445	HepG2	liver:	n/a	n/a
19	PBX3	chr6:142619043-142619967	SK-N-SH	brain:	n/a	n/a
20	EP300	chr6:142619091-142620026	SK-N-SH	brain:	n/a	n/a
21	TEAD4	chr6:142619046-142619563	A549	lung:	n/a	n/a
22	MBD4	chr6:142618054-142619679	HepG2	liver:	n/a	n/a
23	NR3C1	chr6:142619109-142619708	A549	lung:	n/a	n/a
24	EP300	chr6:142618965-142619733	A549	lung:	n/a	n/a
25	NFIC	chr6:142619007-142619712	HepG2	liver:	n/a	n/a
26	MXI1	chr6:142619021-142619979	IMR90	lung:	n/a	n/a
27	USF1	chr6:142619264-142619526	SK-N-SH_RA	brain:	n/a	chr6:142619402-142619413
28	MAX	chr6:142619235-142619847	SK-N-SH	brain:	n/a	n/a
29	HDAC2	chr6:142618979-142619603	HepG2	liver:	n/a	n/a
30	SP1	chr6:142619001-142619656	A549	lung:	n/a	n/a
31	SP1	chr6:142618987-142619634	HepG2	liver:	n/a	n/a
32	MAX	chr6:142619119-142619635	A549	lung:	n/a	n/a
33	MXI1	chr6:142619028-142619703	HepG2	liver:	n/a	n/a
34	NFIC	chr6:142619104-142619985	SK-N-SH	brain:	n/a	n/a
35	RCOR1	chr6:142619080-142619564	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:142619274-142619692	HepG2	liver:	n/a	n/a
37	USF1	chr6:142619293-142619535	SK-N-SH_RA	brain:	n/a	chr6:142619402-142619413
38	HNF4A	chr6:142618981-142619509	HepG2	liver:	n/a	n/a
39	EP300	chr6:142619166-142620046	SK-N-SH	brain:	n/a	n/a
40	FOXA1	chr6:142619117-142619444	T-47D	breast:	n/a	n/a
41	MAFK	chr6:142619228-142619953	IMR90	lung:	n/a	chr6:142619778-142619789 chr6:142619778-142619789 chr6:142619779-142619790 chr6:142619777-142619791
42	FOS	chr6:142619147-142619964	MCF10A-Er-Src	breast:	n/a	n/a
43	FOXA1	chr6:142619034-142619517	A549	lung:	n/a	n/a
44	CREB1	chr6:142619273-142619487	A549	lung:	n/a	n/a
45	TEAD4	chr6:142619107-142620085	SK-N-SH	brain:	n/a	n/a
46	CEBPB	chr6:142619198-142619445	HepG2	liver:	n/a	n/a
47	HNF4G	chr6:142619072-142619521	HepG2	liver:	n/a	n/a
48	PBX3	chr6:142619060-142620115	SK-N-SH	brain:	n/a	n/a
49	NFIC	chr6:142618942-142619705	HepG2	liver:	n/a	n/a
50	SIN3AK20	chr6:142619179-142619606	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:142616393..142621187-chr6:142621251..142624872,10	MCF-7	breast:
2	chr6:142617568..142620556-chr6:142699575..142701431,2	MCF-7	breast:
3	chr6:142604317..142606541-chr6:142618207..142619973,2	MCF-7	breast:
4	chr6:142546061..142548979-chr6:142618829..142620603,2	MCF-7	breast:
5	chr6:142614542..142616316-chr6:142618256..142620564,2	K562	blood:

No data

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs57244265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59280767	0.92[AMR][1000 genomes]
rs59648555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60258191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61299002	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6905012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6906368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6906539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6920468	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6920602	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6926685	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576325	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576330	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1029666	chr6:142594099-142643084	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142616400-142621800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:142617800-142620000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:142618000-142620400	Flanking Active TSS	HepG2	liver
4	chr6:142618200-142619800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr6:142618200-142620000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:142618200-142621800	Enhancers	HMEC	breast
7	chr6:142618400-142619400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:142618400-142619400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr6:142618400-142620400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:142618400-142620400	Enhancers	NHLF	lung
11	chr6:142618400-142620600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:142618400-142621600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:142618400-142621600	Enhancers	NHEK	skin
14	chr6:142618600-142619400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:142618600-142619600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:142618600-142619600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:142618600-142619800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:142618600-142620400	Enhancers	HUVEC	blood vessel
19	chr6:142618600-142620600	Enhancers	HSMM	muscle
20	chr6:142618600-142621800	Weak transcription	Stomach Mucosa	stomach
21	chr6:142618800-142619400	Weak transcription	Placenta	Placenta
22	chr6:142618800-142620000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:142618800-142621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:142618800-142622000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:142619000-142619600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr6:142619000-142619600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:142619000-142619600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:142619000-142619600	Enhancers	NHDF-Ad	bronchial
29	chr6:142619000-142619800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:142619000-142619800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:142619000-142619800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:142619000-142619800	Enhancers	HSMMtube	muscle
33	chr6:142619000-142620000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:142619200-142619600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr6:142619200-142619600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:142619200-142619600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr6:142619200-142619600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:142619200-142619600	Enhancers	Fetal Lung	lung
39	chr6:142619200-142619600	Flanking Active TSS	A549	lung
40	chr6:142619200-142619800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:142619200-142619800	Enhancers	NH-A	brain
42	chr6:142619200-142620000	Enhancers	Osteobl	bone
43	chr6:142619200-142620400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:142619200-142622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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