Variant report

Variant	rs11973620
Chromosome Location	chr7:25608070-25608071
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	BHLHE40	chr7:25608040-25608849	HepG2	liver:	n/a	n/a
2	NR3C1	chr7:25607916-25608538	A549	lung:	n/a	n/a
3	ARID3A	chr7:25608009-25608865	HepG2	liver:	n/a	n/a
4	NR3C1	chr7:25608023-25608410	A549	lung:	n/a	n/a
5	SP1	chr7:25608013-25608857	A549	lung:	n/a	chr7:25608563-25608577
6	FOXA2	chr7:25607924-25608415	A549	lung:	n/a	n/a
7	MAX	chr7:25608018-25608851	MCF-7	breast:	n/a	n/a
8	MAX	chr7:25608064-25608885	A549	lung:	n/a	n/a
9	CTCF	chr7:25607988-25608956	SK-N-SH	brain:	n/a	chr7:25608687-25608696 chr7:25608392-25608400 chr7:25608682-25608698 chr7:25608681-25608699
10	FOXA1	chr7:25608048-25608398	T-47D	breast:	n/a	n/a
11	FOXA1	chr7:25608057-25608404	HepG2	liver:	n/a	n/a
12	FOXA2	chr7:25608037-25608434	HepG2	liver:	n/a	n/a
13	FOXA2	chr7:25608045-25608400	A549	lung:	n/a	n/a
14	NR3C1	chr7:25607948-25608406	A549	lung:	n/a	n/a
15	FOXA1	chr7:25607962-25608527	HepG2	liver:	n/a	n/a
16	CTCF	chr7:25607849-25609048	A549	lung:	n/a	chr7:25608687-25608696 chr7:25608392-25608400 chr7:25608682-25608698 chr7:25608681-25608699
17	RCOR1	chr7:25608063-25608822	HepG2	liver:	n/a	n/a
18	CREB1	chr7:25607934-25608880	HepG2	liver:	n/a	n/a
19	USF1	chr7:25608058-25608525	A549	lung:	n/a	chr7:25608333-25608344
20	MAX	chr7:25607899-25608912	A549	lung:	n/a	n/a
21	ELF1	chr7:25608018-25608886	MCF-7	breast:	n/a	n/a
22	NR3C1	chr7:25607862-25608490	A549	lung:	n/a	n/a
23	FOXA1	chr7:25607959-25608444	A549	lung:	n/a	n/a
24	FOXA1	chr7:25607991-25608505	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000222101	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11973587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973605	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12669889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12670768	0.85[CHB][hapmap]
rs16873895	0.85[CHB][hapmap]
rs17151904	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1818146	0.85[CHB][hapmap]
rs28473276	0.88[ASN][1000 genomes]
rs2952523	0.82[ASN][1000 genomes]
rs2960821	0.90[CHB][hapmap];0.81[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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25604600-25608200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:25604800-25608200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:25607800-25608800	Enhancers	Stomach Mucosa	stomach
4	chr7:25608000-25608200	Enhancers	Liver	Liver
5	chr7:25608000-25608200	Enhancers	Colon Smooth Muscle	Colon
6	chr7:25608000-25608200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr7:25608000-25608200	Enhancers	HepG2	liver
8	chr7:25608000-25608200	Enhancers	K562	blood
9	chr7:25608000-25608400	Enhancers	Fetal Heart	heart
10	chr7:25608000-25608400	Enhancers	Fetal Lung	lung
11	chr7:25608000-25608600	Flanking Active TSS	A549	lung
12	chr7:25608000-25608800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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