Variant report

Variant	rs56316071
Chromosome Location	chr3:28279759-28279760
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	FOXA1	chr3:28279530-28279901	HepG2	liver:	n/a	n/a
2	FOXA2	chr3:28279543-28279774	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:28279547-28279828	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:28274252..28277050-chr3:28277888..28279763,2	MCF-7	breast:
2	chr3:28270292..28273085-chr3:28279670..28282869,3	MCF-7	breast:
3	chr3:28279618..28281224-chr3:28281299..28282942,2	MCF-7	breast:

Variant related genes	Relation type
CMC1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510608	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11914283	1.00[EUR][1000 genomes]
rs11914462	1.00[EUR][1000 genomes]
rs11914828	1.00[EUR][1000 genomes]
rs11917441	1.00[EUR][1000 genomes]
rs11921493	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923319	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11924235	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17021276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17021326	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1845166	0.85[AFR][1000 genomes]
rs1955313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34490679	1.00[EUR][1000 genomes]
rs4680903	0.84[AFR][1000 genomes]
rs55859737	1.00[EUR][1000 genomes]
rs55983177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56854865	1.00[EUR][1000 genomes]
rs59014991	1.00[EUR][1000 genomes]
rs59574091	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60199196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60457049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60812941	1.00[EUR][1000 genomes]
rs61107194	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61120501	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6796693	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72898218	0.92[AFR][1000 genomes]
rs72898222	0.92[AFR][1000 genomes]
rs73822328	1.00[EUR][1000 genomes]
rs73822329	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73822336	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73822564	0.94[AFR][1000 genomes]
rs73822566	0.85[AMR][1000 genomes]
rs73822577	1.00[EUR][1000 genomes]
rs73822578	1.00[EUR][1000 genomes]
rs73825127	1.00[EUR][1000 genomes]
rs73825128	1.00[EUR][1000 genomes]
rs73825130	1.00[EUR][1000 genomes]
rs73825142	1.00[EUR][1000 genomes]
rs73825144	1.00[EUR][1000 genomes]
rs73825146	1.00[EUR][1000 genomes]
rs73825147	1.00[EUR][1000 genomes]
rs73825148	1.00[EUR][1000 genomes]
rs73825149	1.00[EUR][1000 genomes]
rs73825152	1.00[EUR][1000 genomes]
rs73825156	1.00[EUR][1000 genomes]
rs73825163	1.00[EUR][1000 genomes]
rs73825165	1.00[EUR][1000 genomes]
rs73825167	1.00[EUR][1000 genomes]
rs7642252	1.00[EUR][1000 genomes]
rs7642709	1.00[EUR][1000 genomes]
rs9682725	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876648	chr3:28060456-28280965	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28270000-28280800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:28271800-28280600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:28273800-28281200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:28274200-28282000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:28277400-28282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:28279000-28281800	Weak transcription	Primary T cells from cord blood	blood
7	chr3:28279200-28282000	Weak transcription	NHDF-Ad	bronchial
8	chr3:28279600-28279800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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