Variant report

Variant	rs4961725
Chromosome Location	chr9:16599255-16599256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10116857	0.85[EUR][1000 genomes]
rs10118895	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10120002	0.82[MEX][hapmap]
rs10120281	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10122372	0.90[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10124530	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10125014	1.00[CEU][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs1029016	0.81[AMR][1000 genomes]
rs10511622	0.85[TSI][hapmap]
rs10733311	0.85[AMR][1000 genomes]
rs10733312	0.91[EUR][1000 genomes]
rs10738437	0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10738439	0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs10738440	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10738441	0.88[AMR][1000 genomes]
rs10756764	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10756765	1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs10756766	0.88[AMR][1000 genomes]
rs10756768	0.85[AMR][1000 genomes]
rs10756770	0.88[AMR][1000 genomes]
rs10962484	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10962510	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12000426	1.00[CEU][hapmap]
rs12004304	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12337676	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12339625	1.00[CEU][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12350242	0.85[EUR][1000 genomes]
rs1337393	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1337400	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1415475	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1415476	0.90[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1538102	0.84[EUR][1000 genomes]
rs16934816	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16934842	0.85[EUR][1000 genomes]
rs16934855	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16934875	0.82[MEX][hapmap]
rs16934886	0.84[EUR][1000 genomes]
rs17738890	0.84[EUR][1000 genomes]
rs1927626	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2095657	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2149159	0.83[EUR][1000 genomes]
rs28428651	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28457730	0.88[AMR][1000 genomes]
rs28490464	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28501274	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28648047	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28651010	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4466493	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56218971	0.84[EUR][1000 genomes]
rs7018743	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7018877	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7019016	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7019105	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7019625	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7032239	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7032523	1.00[CEU][hapmap]
rs7032772	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7034606	0.85[AMR][1000 genomes]
rs7035303	0.92[AMR][1000 genomes]
rs7036282	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7048399	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7048805	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7049170	0.82[EUR][1000 genomes]
rs725011	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73417477	0.86[EUR][1000 genomes]
rs7470623	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7854979	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7856477	0.83[EUR][1000 genomes]
rs7859395	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7859971	0.85[AMR][1000 genomes]
rs7870508	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7870730	0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs7873338	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv524264	chr9:16596071-16611692	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16576000-16601600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:16576400-16601400	Weak transcription	NHDF-Ad	bronchial
3	chr9:16583000-16606800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:16583200-16611200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:16586800-16604400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:16594800-16601800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:16594800-16601800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:16595000-16611200	Weak transcription	NHLF	lung
9	chr9:16597600-16601400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:16597600-16604400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:16597600-16610800	Weak transcription	Fetal Stomach	stomach
12	chr9:16598000-16599400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:16598200-16599400	Enhancers	Fetal Lung	lung
14	chr9:16598400-16599600	Enhancers	NHEK	skin
15	chr9:16598600-16599400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:16598600-16599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:16598800-16601600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:16598800-16608200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:16598800-16611400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:16599000-16599400	Weak transcription	Ovary	ovary
21	chr9:16599000-16603600	Weak transcription	A549	lung
22	chr9:16599000-16607000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:16599000-16612200	Weak transcription	Osteobl	bone
24	chr9:16599000-16612600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links