Variant report

Variant	rs9403522
Chromosome Location	chr6:143994708-143994709
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	NFIC	chr6:143994584-143995360	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr6:143994627-143995380	ECC-1	luminal epithelium:	n/a	n/a
3	SP1	chr6:143994556-143995443	HCT-116	colon:	n/a	chr6:143994940-143994949
4	TCF12	chr6:143994574-143995313	ECC-1	luminal epithelium:	n/a	n/a
5	FOSL1	chr6:143994639-143995312	HCT-116	colon:	n/a	n/a
6	FOS	chr6:143994677-143995347	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr6:143994591-143995465	MCF-7	breast:	n/a	chr6:143995386-143995393
8	TCF12	chr6:143994548-143995451	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr6:143994682-143995328	SK-N-SH	brain:	n/a	n/a
10	EP300	chr6:143994532-143995379	ECC-1	luminal epithelium:	n/a	chr6:143995296-143995306
11	PBX3	chr6:143994701-143995222	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr6:143994542-143995360	ECC-1	luminal epithelium:	n/a	chr6:143995112-143995121
13	FOSL1	chr6:143994556-143995310	HCT-116	colon:	n/a	n/a
14	POLR2A	chr6:143994660-143995322	HUVEC	blood vessel:	n/a	n/a
15	RAD21	chr6:143994686-143995249	ECC-1	luminal epithelium:	n/a	n/a
16	SP1	chr6:143994644-143995170	A549	lung:	n/a	chr6:143994940-143994949
17	POLR2A	chr6:143994708-143995020	ECC-1	luminal epithelium:	n/a	n/a
18	JUND	chr6:143994708-143995267	MCF-7	breast:	n/a	n/a
19	FOXM1	chr6:143993964-143995490	ECC-1	luminal epithelium:	n/a	n/a
20	TEAD4	chr6:143994611-143995323	ECC-1	luminal epithelium:	n/a	chr6:143995112-143995121
21	FOSL2	chr6:143994693-143995215	A549	lung:	n/a	n/a
22	EP300	chr6:143994648-143995220	A549	lung:	n/a	n/a
23	ESR1	chr6:143994705-143995188	ECC-1	luminal epithelium:	n/a	n/a
24	CEBPB	chr6:143994684-143995307	MCF-7	breast:	n/a	n/a
25	FOSL2	chr6:143994677-143995243	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr6:143994679-143995312	MCF-7	breast:	n/a	n/a
27	USF1	chr6:143994644-143995184	HCT-116	colon:	n/a	chr6:143994920-143994941
28	SRF	chr6:143994683-143995211	ECC-1	luminal epithelium:	n/a	n/a
29	NFIC	chr6:143994514-143995437	ECC-1	luminal epithelium:	n/a	n/a
30	EP300	chr6:143993892-143995949	ECC-1	luminal epithelium:	n/a	chr6:143995296-143995306
31	TCF12	chr6:143994650-143995260	A549	lung:	n/a	n/a
32	USF1	chr6:143994646-143995141	H1-hESC	embryonic stem cell:	n/a	chr6:143994920-143994941
33	E2F4	chr6:143994339-143995119	MCF10A-Er-Src	breast:	n/a	n/a
34	CEBPB	chr6:143994094-143995421	HCT-116	colon:	n/a	n/a
35	FOXM1	chr6:143994437-143995474	ECC-1	luminal epithelium:	n/a	n/a
36	SP1	chr6:143994584-143995430	HCT-116	colon:	n/a	chr6:143994940-143994949
37	JUND	chr6:143994651-143995361	HCT-116	colon:	n/a	n/a
38	USF1	chr6:143994678-143995245	ECC-1	luminal epithelium:	n/a	chr6:143994920-143994941
39	EP300	chr6:143994686-143995278	A549	lung:	n/a	n/a
40	FOSL2	chr6:143994708-143995277	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:143993420..143996184-chr6:143997864..144000506,3	MCF-7	breast:
2	chr6:143994499..143997222-chr6:144164317..144166066,3	MCF-7	breast:
3	chr6:143993920..143996702-chr6:144021547..144023983,2	MCF-7	breast:
4	chr6:143993282..143995063-chr6:144073784..144075986,2	MCF-7	breast:

Variant related genes	Relation type
PHACTR2	TF binding region
ENSG00000135521	Chromatin interaction
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11155318	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11155320	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11962519	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12530310	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13190772	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13191259	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204954	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220613	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2051008	0.88[ASN][1000 genomes]
rs2092762	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474150	0.88[ASN][1000 genomes]
rs3924968	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4299843	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4523103	0.97[EUR][1000 genomes]
rs6570571	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570572	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570573	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913687	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914940	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916245	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6931556	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7450663	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7738179	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740883	0.83[ASN][1000 genomes]
rs7741628	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7741901	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741998	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7747182	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7758298	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760178	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762598	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7764549	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766091	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7770812	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7772898	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910419	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9321933	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9321934	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9376773	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376774	0.86[EUR][1000 genomes]
rs9376775	0.86[EUR][1000 genomes]
rs9376777	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390127	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399454	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399456	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403520	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9484794	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9496718	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496721	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9496729	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496734	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9496735	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143993400-143995600	Weak transcription	Aorta	Aorta
2	chr6:143993600-143996400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:143993600-143996800	Enhancers	Placenta	Placenta
4	chr6:143994000-143996200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:143994000-143997800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:143994000-143998800	Enhancers	Hela-S3	cervix
7	chr6:143994200-143994800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:143994200-143994800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:143994200-143994800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:143994200-143994800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:143994200-143995000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:143994200-143995200	Enhancers	Fetal Intestine Small	intestine
13	chr6:143994200-143995200	Enhancers	K562	blood
14	chr6:143994200-143995800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:143994200-143995800	Enhancers	HSMM	muscle
16	chr6:143994200-143996000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:143994200-143996000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:143994200-143996000	Enhancers	NH-A	brain
19	chr6:143994200-143996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:143994200-143996400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:143994200-143996400	Enhancers	Osteobl	bone
22	chr6:143994200-143996600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:143994200-143996800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:143994200-143996800	Enhancers	Fetal Muscle Leg	muscle
25	chr6:143994200-143996800	Enhancers	Fetal Stomach	stomach
26	chr6:143994200-143996800	Enhancers	Gastric	stomach
27	chr6:143994200-143997000	Enhancers	Stomach Mucosa	stomach
28	chr6:143994200-143997400	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:143994200-143997600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:143994200-143997800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:143994200-143998000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:143994200-143998000	Enhancers	Fetal Kidney	kidney
33	chr6:143994200-143998000	Enhancers	NHDF-Ad	bronchial
34	chr6:143994200-143998000	Enhancers	NHLF	lung
35	chr6:143994200-143998200	Enhancers	HMEC	breast
36	chr6:143994200-143998400	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr6:143994200-143998600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:143994200-143998600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:143994200-143998600	Enhancers	HepG2	liver
40	chr6:143994200-143999000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:143994400-143995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:143994400-143995400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:143994400-143995600	Weak transcription	Esophagus	oesophagus
44	chr6:143994400-143995800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:143994400-143997600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr6:143994600-143994800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:143994600-143994800	Flanking Active TSS	A549	lung
48	chr6:143994600-143994800	Flanking Active TSS	NHEK	skin
49	chr6:143994600-143995000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:143994600-143995000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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