Variant report

Variant	rs9864984
Chromosome Location	chr3:89428776-89428777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1398534	0.82[CEU][hapmap]
rs1512185	0.80[ASN][1000 genomes]
rs17738248	0.81[CEU][hapmap]
rs17800551	0.81[CEU][hapmap]
rs17801001	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17801031	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2063590	0.82[CEU][hapmap]
rs2175670	0.82[CEU][hapmap]
rs28623022	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4857497	0.81[CEU][hapmap]
rs4857502	0.86[CEU][hapmap]
rs57670516	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62275015	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62275016	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62275018	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62275019	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773815	0.81[CEU][hapmap]
rs6782527	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800041	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137381	0.81[ASN][1000 genomes]
rs73137382	0.81[ASN][1000 genomes]
rs73137384	0.84[ASN][1000 genomes]
rs73137387	0.81[ASN][1000 genomes]
rs73137393	0.81[ASN][1000 genomes]
rs73137395	0.84[ASN][1000 genomes]
rs7615949	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631682	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645408	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870898	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870899	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829401	0.81[CEU][hapmap]
rs9832305	0.95[CEU][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9836340	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842599	0.95[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9844971	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849029	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852380	0.82[CEU][hapmap]
rs9852722	0.82[CEU][hapmap]
rs9854073	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860266	0.95[CEU][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862195	0.82[CEU][hapmap]
rs9863058	0.82[CEU][hapmap]
rs9863107	0.82[CEU][hapmap]
rs9866618	0.81[CEU][hapmap]
rs9868782	0.80[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875278	0.86[CEU][hapmap]
rs993186	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1001345	chr3:89368629-89444995	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1000694	chr3:89373820-89453045	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1011402	chr3:89384121-89444995	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv590928	chr3:89389507-89442369	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1012824	chr3:89394580-89431445	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv516852	chr3:89402447-89442369	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1002605	chr3:89413038-89453045	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89417800-89433600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:89422800-89429000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:89426000-89429200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:89426000-89429800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:89426800-89429000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:89426800-89429600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:89427600-89429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:89427600-89429400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:89427800-89429200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:89427800-89429600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:89427800-89429600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:89428200-89435200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:89428600-89429000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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