Variant report

Variant	rs56890199
Chromosome Location	chr3:161035938-161035939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161030291..161037720-chr3:161038093..161046558,15	MCF-7	breast:
2	chr3:161033236..161036164-chr3:161124055..161126623,3	MCF-7	breast:
3	chr3:161026332..161029255-chr3:161034425..161036502,2	MCF-7	breast:
4	chr3:161031627..161035949-chr3:161055362..161059558,6	MCF-7	breast:
5	chr3:160998590..161004098-chr3:161031167..161035957,5	MCF-7	breast:
6	chr3:160991443..160993916-chr3:161034592..161038621,3	MCF-7	breast:
7	chr3:161030909..161038608-chr3:161038848..161046580,20	MCF-7	breast:
8	chr3:161006401..161012112-chr3:161031973..161037314,13	MCF-7	breast:
9	chr3:160980180..160982518-chr3:161034107..161036039,2	MCF-7	breast:
10	chr3:161025819..161030681-chr3:161030815..161036788,8	MCF-7	breast:
11	chr3:161034414..161036485-chr3:161127790..161130788,3	MCF-7	breast:
12	chr3:161023015..161026193-chr3:161034536..161038815,6	MCF-7	breast:
13	chr3:161026928..161036306-chr3:161081784..161094254,31	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240138	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12108169	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374001	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12629152	0.89[AMR][1000 genomes]
rs12629929	0.85[ASN][1000 genomes]
rs12630038	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632346	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633103	0.90[ASN][1000 genomes]
rs12636434	0.90[ASN][1000 genomes]
rs12636573	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12636590	0.89[AMR][1000 genomes]
rs1478568	0.80[ASN][1000 genomes]
rs16834031	0.90[ASN][1000 genomes]
rs1904204	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28853731	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4132373	0.89[AMR][1000 genomes]
rs55949838	0.90[ASN][1000 genomes]
rs56741879	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57441646	0.90[ASN][1000 genomes]
rs59827519	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60228180	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60277631	0.84[AMR][1000 genomes]
rs60801542	0.89[AMR][1000 genomes]
rs61193379	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61578814	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61596736	0.89[AMR][1000 genomes]
rs73875458	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73875472	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73875473	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73875482	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875492	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875500	0.83[ASN][1000 genomes]
rs73875502	0.83[ASN][1000 genomes]
rs73878303	0.83[ASN][1000 genomes]
rs73878304	0.81[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161035000-161036400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:161035800-161036200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links