Variant report

Variant	rs72827727
Chromosome Location	chr2:99394902-99394903
allele	A/G
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	EP300	chr2:99394559-99395095	ECC-1	luminal epithelium:	n/a	chr2:99394843-99394852
2	NFIC	chr2:99394452-99395213	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr2:99394534-99395172	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr2:99394568-99395083	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr2:99394416-99395059	ECC-1	luminal epithelium:	n/a	chr2:99394634-99394647 chr2:99394634-99394647 chr2:99394634-99394642 chr2:99394636-99394645 chr2:99394639-99394647 chr2:99394634-99394647
6	NFIC	chr2:99394414-99395119	ECC-1	luminal epithelium:	n/a	n/a
7	CEBPB	chr2:99394584-99395027	ECC-1	luminal epithelium:	n/a	chr2:99394892-99394905
8	EP300	chr2:99394518-99395171	ECC-1	luminal epithelium:	n/a	chr2:99394843-99394852
9	STAT3	chr2:99394682-99394973	MCF10A-Er-Src	breast:	n/a	chr2:99394842-99394851 chr2:99394830-99394839 chr2:99394831-99394840 chr2:99394828-99394842
10	TEAD4	chr2:99394585-99395055	ECC-1	luminal epithelium:	n/a	n/a
11	STAT3	chr2:99394694-99394973	MCF10A-Er-Src	breast:	n/a	chr2:99394842-99394851 chr2:99394830-99394839 chr2:99394831-99394840 chr2:99394828-99394842
12	TCF12	chr2:99394507-99395086	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99384896..99387607-chr2:99394803..99397192,2	MCF-7	breast:
2	chr2:99393178..99396071-chr2:99408635..99411955,5	MCF-7	breast:
3	chr2:99391084..99393411-chr2:99394844..99396426,2	MCF-7	breast:

Variant related genes	Relation type
RNU4-84P	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10496330	0.86[EUR][1000 genomes]
rs1877905	0.86[EUR][1000 genomes]
rs2090181	0.81[ASN][1000 genomes]
rs2203432	0.81[ASN][1000 genomes]
rs2871243	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2871244	0.81[ASN][1000 genomes]
rs3731660	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4851160	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs57185248	0.87[ASN][1000 genomes]
rs58516468	0.87[ASN][1000 genomes]
rs58560917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58676789	0.83[ASN][1000 genomes]
rs59083513	0.81[ASN][1000 genomes]
rs59313126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59989465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60496162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61042973	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61311613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61359279	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61402919	0.81[ASN][1000 genomes]
rs72811003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72811004	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72811005	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825780	0.86[EUR][1000 genomes]
rs72825782	0.86[EUR][1000 genomes]
rs72825784	0.86[EUR][1000 genomes]
rs72825789	0.86[EUR][1000 genomes]
rs72825790	0.86[EUR][1000 genomes]
rs72825800	0.86[EUR][1000 genomes]
rs72825801	0.86[EUR][1000 genomes]
rs72827704	0.86[EUR][1000 genomes]
rs72827705	0.86[EUR][1000 genomes]
rs72827707	0.86[EUR][1000 genomes]
rs72827708	0.86[EUR][1000 genomes]
rs72827713	0.86[EUR][1000 genomes]
rs72827717	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827722	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827724	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827726	0.87[ASN][1000 genomes]
rs72827728	0.84[ASN][1000 genomes]
rs72827729	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827736	0.83[ASN][1000 genomes]
rs72827739	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827740	0.81[ASN][1000 genomes]
rs72827741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827742	0.81[ASN][1000 genomes]
rs72827743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
2	chr2:99391000-99395400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:99391600-99406600	Weak transcription	Thymus	Thymus
4	chr2:99392800-99396200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99394400-99396000	Enhancers	HepG2	liver
6	chr2:99394800-99395000	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links