Variant report

Variant	rs298548
Chromosome Location	chr5:17360355-17360356
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:17216728..17218408-chr5:17358754..17361119,2	MCF-7	breast:
2	chr5:17306150..17307962-chr5:17359469..17361900,2	MCF-7	breast:
3	chr5:17336392..17339049-chr5:17358419..17360973,2	MCF-7	breast:
4	chr5:17358851..17361817-chr5:17363155..17365630,2	K562	blood:

Variant related genes	Relation type
ENSG00000176788	Chromatin interaction
ENSG00000215196	Chromatin interaction
ENSG00000185296	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10074496	0.89[EUR][1000 genomes]
rs10462609	0.89[EUR][1000 genomes]
rs11950287	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13355635	0.89[EUR][1000 genomes]
rs182441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1827400	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2134241	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2134242	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2173968	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2454946	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2650923	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650935	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650936	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650937	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650938	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650939	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650940	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650942	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650943	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650944	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650945	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652638	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652639	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652643	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652644	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652645	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652646	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652647	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2652648	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28476505	0.87[EUR][1000 genomes]
rs298530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298531	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298532	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298534	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298535	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298536	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298558	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298559	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298560	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298562	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299384	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299385	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299386	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56663279	0.90[EUR][1000 genomes]
rs56705013	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58062922	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58468495	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6862515	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73052871	0.89[EUR][1000 genomes]
rs73052881	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73052887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73052888	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73052898	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73052901	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73054809	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73054823	0.90[EUR][1000 genomes]
rs7719794	0.90[EUR][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	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr5:17354800-17366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:17359000-17360800	Enhancers	NHDF-Ad	bronchial
3	chr5:17359400-17360800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:17359600-17360400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr5:17359600-17361800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr5:17359800-17360600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:17359800-17362600	Enhancers	Placenta	Placenta
8	chr5:17360000-17360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:17360000-17360400	Flanking Active TSS	Osteobl	bone
10	chr5:17360000-17360600	Enhancers	Fetal Muscle Leg	muscle
11	chr5:17360000-17360800	Enhancers	NHLF	lung
12	chr5:17360000-17361600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:17360200-17360400	Enhancers	HSMM	muscle
14	chr5:17360200-17360600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:17360200-17360600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:17360200-17360800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:17360200-17360800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:17360200-17361600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links