Variant report

Variant	rs28473276
Chromosome Location	chr7:25608535-25608536
allele	G/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	CTCF	chr7:25608534-25608849	A549	lung:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
2	USF1	chr7:25608096-25608541	A549	lung:	n/a	chr7:25608333-25608344
3	SMC3	chr7:25608128-25608872	HepG2	liver:	n/a	chr7:25608683-25608697
4	BHLHE40	chr7:25608040-25608849	HepG2	liver:	n/a	n/a
5	RAD21	chr7:25608499-25608857	MCF-7	breast:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
6	FOXA2	chr7:25608447-25608815	A549	lung:	n/a	n/a
7	FOXA1	chr7:25608460-25608852	T-47D	breast:	n/a	n/a
8	CTCF	chr7:25608500-25608650	HFF-Myc	foreskin:	n/a	n/a
9	RAD21	chr7:25608493-25608797	GM12878	blood:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
10	RAD21	chr7:25608485-25608879	SK-N-SH_RA	brain:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
11	CUX1	chr7:25608323-25608957	K562	blood:	n/a	n/a
12	GTF2F1	chr7:25608535-25608835	H1-hESC	embryonic stem cell:	n/a	n/a
13	NR3C1	chr7:25607916-25608538	A549	lung:	n/a	n/a
14	GATA3	chr7:25608470-25608807	T-47D	breast:	n/a	n/a
15	ELF1	chr7:25608184-25608889	HCT-116	colon:	n/a	n/a
16	CTCF	chr7:25608432-25608943	MCF-7	breast:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
17	ELF1	chr7:25608438-25608858	HepG2	liver:	n/a	n/a
18	HCFC1	chr7:25608523-25608854	K562	blood:	n/a	n/a
19	RAD21	chr7:25608467-25608894	H1-hESC	embryonic stem cell:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
20	RAD21	chr7:25608398-25608891	H1-hESC	embryonic stem cell:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
21	MAX	chr7:25608160-25608649	HepG2	liver:	n/a	n/a
22	CTCF	chr7:25608460-25608610	A549	lung:	n/a	n/a
23	JUND	chr7:25608211-25608821	HepG2	liver:	n/a	chr7:25608363-25608374 chr7:25608364-25608374 chr7:25608365-25608373 chr7:25608364-25608374 chr7:25608358-25608370
24	ARID3A	chr7:25608009-25608865	HepG2	liver:	n/a	n/a
25	RAD21	chr7:25608501-25608832	HepG2	liver:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
26	FOXA1	chr7:25608410-25608820	T-47D	breast:	n/a	n/a
27	CTCF	chr7:25608485-25608866	A549	lung:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
28	CTCF	chr7:25608400-25608550	GM12873	blood:	n/a	n/a
29	ELF1	chr7:25608376-25608866	A549	lung:	n/a	n/a
30	CTCF	chr7:25608520-25608670	HFF-Myc	foreskin:	n/a	n/a
31	SP1	chr7:25608013-25608857	A549	lung:	n/a	chr7:25608563-25608577
32	YY1	chr7:25608516-25608829	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr7:25608346-25608962	HCT-116	colon:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
34	RAD21	chr7:25608493-25608768	SK-N-SH_RA	brain:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
35	RAD21	chr7:25608516-25608828	HepG2	liver:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
36	ELK1	chr7:25608466-25608809	K562	blood:	n/a	n/a
37	RCOR1	chr7:25608491-25608821	K562	blood:	n/a	n/a
38	BHLHE40	chr7:25608184-25608761	A549	lung:	n/a	n/a
39	MAX	chr7:25608076-25608769	K562	blood:	n/a	n/a
40	CTCF	chr7:25608530-25608857	MCF-7	breast:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
41	MAX	chr7:25608018-25608851	MCF-7	breast:	n/a	n/a
42	MAX	chr7:25608064-25608885	A549	lung:	n/a	n/a
43	CTCF	chr7:25608485-25608826	A549	lung:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
44	USF2	chr7:25608137-25608670	HepG2	liver:	n/a	n/a
45	CTCF	chr7:25607988-25608956	SK-N-SH	brain:	n/a	chr7:25608687-25608696 chr7:25608392-25608400 chr7:25608682-25608698 chr7:25608681-25608699
46	RAD21	chr7:25608295-25608850	A549	lung:	n/a	chr7:25608683-25608693 chr7:25608679-25608698
47	CTCF	chr7:25608471-25608906	T-47D	breast:	n/a	chr7:25608687-25608696 chr7:25608682-25608698 chr7:25608681-25608699
48	ZNF143	chr7:25608423-25608860	K562	blood:	n/a	n/a
49	ELF1	chr7:25608221-25608889	A549	lung:	n/a	n/a
50	ARID3A	chr7:25608534-25608799	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:25299061..25300348-chr7:25608226..25609143,4	K562	blood:
2	chr7:25430704..25431525-chr7:25608219..25609114,4	K562	blood:
3	chr7:25608198..25609026-chr7:25891099..25891911,6	MCF-7	breast:
4	chr7:25429098..25432014-chr7:25608292..25610212,2	K562	blood:
5	chr7:25430634..25431513-chr7:25608350..25609015,3	MCF-7	breast:
6	chr7:25256547..25257067-chr7:25608230..25609163,2	K562	blood:

Variant related genes	Relation type
ENSG00000222101	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10486406	0.88[ASN][1000 genomes]
rs10951078	0.88[ASN][1000 genomes]
rs11973587	0.88[ASN][1000 genomes]
rs11973605	0.81[ASN][1000 genomes]
rs11973620	0.88[ASN][1000 genomes]
rs12669889	0.80[ASN][1000 genomes]
rs12670768	0.88[ASN][1000 genomes]
rs1354264	0.88[ASN][1000 genomes]
rs1553399	0.88[ASN][1000 genomes]
rs16873895	0.88[ASN][1000 genomes]
rs16873899	0.88[ASN][1000 genomes]
rs16873909	0.83[ASN][1000 genomes]
rs17151904	0.88[ASN][1000 genomes]
rs1818146	0.88[ASN][1000 genomes]
rs2952523	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2960821	0.90[ASN][1000 genomes]
rs62454590	0.86[ASN][1000 genomes]
rs62454591	0.88[ASN][1000 genomes]
rs62454592	0.88[ASN][1000 genomes]
rs739622	0.88[ASN][1000 genomes]
rs975369	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	nsv525378	chr7:25605725-25615221	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv526019	chr7:25606120-25615221	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv527227	chr7:25606120-25615221	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1797873	chr7:25606956-25615898	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25607800-25608800	Enhancers	Stomach Mucosa	stomach
2	chr7:25608000-25608600	Flanking Active TSS	A549	lung
3	chr7:25608000-25608800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr7:25608200-25608600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr7:25608200-25608600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:25608200-25608600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:25608200-25608600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:25608200-25608600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr7:25608200-25608600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:25608200-25608600	Flanking Active TSS	Liver	Liver
11	chr7:25608200-25608600	Enhancers	Placenta	Placenta
12	chr7:25608200-25608600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr7:25608200-25608600	Flanking Active TSS	HepG2	liver
14	chr7:25608200-25608600	Flanking Active TSS	K562	blood
15	chr7:25608200-25608800	Enhancers	Pancreas	Pancrea
16	chr7:25608200-25609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:25608400-25608600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr7:25608400-25608600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr7:25608400-25609200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:25608400-25613400	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links