Variant report

Variant	rs17404262
Chromosome Location	chr15:49967619-49967620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49916467..49919057-chr15:49966051..49969032,2	MCF-7	breast:
2	chr15:49911826..49914889-chr15:49965782..49969006,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166262	Chromatin interaction
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10519233	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070707	0.82[CEU][hapmap]
rs13329455	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354918	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588127	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17402569	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17480434	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481696	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483139	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413963	0.82[CEU][hapmap]
rs28393768	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28408092	0.82[EUR][1000 genomes]
rs28409376	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28430272	0.81[EUR][1000 genomes]
rs28465200	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484276	0.82[EUR][1000 genomes]
rs28492008	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28516445	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568399	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635979	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669217	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28671247	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798135	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28843724	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210227	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774539	0.84[CEU][hapmap]
rs8040436	0.81[CEU][hapmap]
rs8040716	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs967892	0.82[CEU][hapmap]
rs967893	0.82[CEU][hapmap]
rs9920574	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920705	0.98[AMR][1000 genomes];0.97[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	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49965400-49968400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49965600-49968000	Enhancers	Hela-S3	cervix
3	chr15:49965600-49968200	Enhancers	HMEC	breast
4	chr15:49965600-49968600	Enhancers	NHDF-Ad	bronchial
5	chr15:49965800-49967800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:49965800-49967800	Enhancers	NHEK	skin
7	chr15:49965800-49968200	Enhancers	Osteobl	bone
8	chr15:49966000-49967800	Enhancers	HSMM	muscle
9	chr15:49966000-49968000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr15:49966000-49968200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:49966600-49968200	Enhancers	HSMMtube	muscle
12	chr15:49966800-49970000	Weak transcription	Ovary	ovary
13	chr15:49966800-49987400	Weak transcription	NHLF	lung
14	chr15:49967200-49967800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr15:49967200-49968000	Enhancers	Colon Smooth Muscle	Colon
16	chr15:49967200-49968200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:49967400-49968200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:49967600-49968200	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links