Variant report

Variant	rs6907410
Chromosome Location	chr6:143995142-143995143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr6:143994734-143995314	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr6:143994584-143995360	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF217	chr6:143994925-143995262	MCF-7	breast:	n/a	n/a
4	CEBPB	chr6:143994627-143995380	ECC-1	luminal epithelium:	n/a	n/a
5	SP1	chr6:143994556-143995443	HCT-116	colon:	n/a	chr6:143994940-143994949
6	GATA3	chr6:143994793-143995210	T-47D	breast:	n/a	n/a
7	SP1	chr6:143994739-143995192	A549	lung:	n/a	chr6:143994940-143994949
8	RAD21	chr6:143994765-143995194	ECC-1	luminal epithelium:	n/a	n/a
9	YY1	chr6:143994771-143995160	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr6:143994574-143995313	ECC-1	luminal epithelium:	n/a	n/a
11	FOSL1	chr6:143994639-143995312	HCT-116	colon:	n/a	n/a
12	FOS	chr6:143994677-143995347	MCF10A-Er-Src	breast:	n/a	n/a
13	GATA3	chr6:143994591-143995465	MCF-7	breast:	n/a	chr6:143995386-143995393
14	SP1	chr6:143994805-143995329	H1-hESC	embryonic stem cell:	n/a	chr6:143994940-143994949
15	HDAC2	chr6:143994780-143995298	MCF-7	breast:	n/a	n/a
16	TCF12	chr6:143994548-143995451	ECC-1	luminal epithelium:	n/a	n/a
17	FOS	chr6:143994730-143995263	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr6:143994793-143995218	MCF10A-Er-Src	breast:	n/a	n/a
19	TCF12	chr6:143994682-143995328	SK-N-SH	brain:	n/a	n/a
20	FOS	chr6:143994811-143995388	HUVEC	blood vessel:	n/a	n/a
21	EP300	chr6:143994532-143995379	ECC-1	luminal epithelium:	n/a	chr6:143995296-143995306
22	MAX	chr6:143994752-143995283	HCT-116	colon:	n/a	chr6:143994925-143994936
23	PBX3	chr6:143994701-143995222	SK-N-SH	brain:	n/a	n/a
24	TEAD4	chr6:143994542-143995360	ECC-1	luminal epithelium:	n/a	chr6:143995112-143995121
25	PBX3	chr6:143994775-143995165	SK-N-SH	brain:	n/a	n/a
26	FOSL1	chr6:143994556-143995310	HCT-116	colon:	n/a	n/a
27	GATA3	chr6:143994773-143995347	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr6:143994660-143995322	HUVEC	blood vessel:	n/a	n/a
29	RAD21	chr6:143994686-143995249	ECC-1	luminal epithelium:	n/a	n/a
30	SP1	chr6:143994644-143995170	A549	lung:	n/a	chr6:143994940-143994949
31	CEBPB	chr6:143994772-143995156	MCF-7	breast:	n/a	n/a
32	POLR2A	chr6:143994731-143995189	MCF10A-Er-Src	breast:	n/a	n/a
33	JUND	chr6:143994836-143995151	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr6:143994708-143995267	MCF-7	breast:	n/a	n/a
35	FOXM1	chr6:143993964-143995490	ECC-1	luminal epithelium:	n/a	n/a
36	SP1	chr6:143994875-143995303	H1-hESC	embryonic stem cell:	n/a	chr6:143994940-143994949
37	TEAD4	chr6:143994611-143995323	ECC-1	luminal epithelium:	n/a	chr6:143995112-143995121
38	POLR2A	chr6:143994791-143995160	HCT-116	colon:	n/a	n/a
39	FOSL2	chr6:143994693-143995215	A549	lung:	n/a	n/a
40	EP300	chr6:143994648-143995220	A549	lung:	n/a	n/a
41	ELF1	chr6:143994744-143995338	MCF-7	breast:	n/a	n/a
42	MYC	chr6:143994779-143995273	MCF10A-Er-Src	breast:	n/a	chr6:143994925-143994936
43	TCF7L2	chr6:143994802-143995187	Hela-S3	cervix:	n/a	n/a
44	JUND	chr6:143994736-143995355	HCT-116	colon:	n/a	n/a
45	REST	chr6:143994753-143995239	ECC-1	luminal epithelium:	n/a	n/a
46	CEBPB	chr6:143994742-143995280	ECC-1	luminal epithelium:	n/a	n/a
47	ESR1	chr6:143994705-143995188	ECC-1	luminal epithelium:	n/a	n/a
48	GATA2	chr6:143994910-143995208	HUVEC	blood vessel:	n/a	n/a
49	CEBPB	chr6:143994684-143995307	MCF-7	breast:	n/a	n/a
50	FOSL2	chr6:143994677-143995243	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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	chr6:143994808..143997283-chr6:143999209..144001887,3	MCF-7	breast:

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10872562	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108314	0.90[ASN][1000 genomes]
rs11155317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198291	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206069	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12207002	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528456	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3924969	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934959	0.81[ASN][1000 genomes]
rs6901659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6913134	0.87[ASN][1000 genomes]
rs6915784	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740709	0.85[ASN][1000 genomes]
rs7741424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748882	0.80[ASN][1000 genomes]
rs7766510	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7769294	0.81[ASN][1000 genomes]
rs7772565	0.82[ASN][1000 genomes]
rs7776119	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8180640	0.90[ASN][1000 genomes]
rs9373396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376779	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386042	0.84[ASN][1000 genomes]
rs9390126	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399458	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403523	0.97[EUR][1000 genomes];0.85[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:68 , 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	chr6:143994200-143995200	Enhancers	Fetal Intestine Small	intestine
8	chr6:143994200-143995200	Enhancers	K562	blood
9	chr6:143994200-143995800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:143994200-143995800	Enhancers	HSMM	muscle
11	chr6:143994200-143996000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:143994200-143996000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:143994200-143996000	Enhancers	NH-A	brain
14	chr6:143994200-143996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:143994200-143996400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:143994200-143996400	Enhancers	Osteobl	bone
17	chr6:143994200-143996600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:143994200-143996800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:143994200-143996800	Enhancers	Fetal Muscle Leg	muscle
20	chr6:143994200-143996800	Enhancers	Fetal Stomach	stomach
21	chr6:143994200-143996800	Enhancers	Gastric	stomach
22	chr6:143994200-143997000	Enhancers	Stomach Mucosa	stomach
23	chr6:143994200-143997400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:143994200-143997600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:143994200-143997800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:143994200-143998000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:143994200-143998000	Enhancers	Fetal Kidney	kidney
28	chr6:143994200-143998000	Enhancers	NHDF-Ad	bronchial
29	chr6:143994200-143998000	Enhancers	NHLF	lung
30	chr6:143994200-143998200	Enhancers	HMEC	breast
31	chr6:143994200-143998400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr6:143994200-143998600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:143994200-143998600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:143994200-143998600	Enhancers	HepG2	liver
35	chr6:143994200-143999000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:143994400-143995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:143994400-143995400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:143994400-143995600	Weak transcription	Esophagus	oesophagus
39	chr6:143994400-143995800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:143994400-143997600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr6:143994600-143995600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:143994600-143995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:143994600-143995600	Weak transcription	Small Intestine	intestine
44	chr6:143994600-143995600	Flanking Active TSS	HUVEC	blood vessel
45	chr6:143994600-143997000	Enhancers	Fetal Intestine Large	intestine
46	chr6:143994600-143997000	Enhancers	Fetal Lung	lung
47	chr6:143994600-143997200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:143994600-143999000	Weak transcription	Lung	lung
49	chr6:143994800-143995200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr6:143994800-143995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links