Variant report

Variant	rs12734357
Chromosome Location	chr1:79839639-79839640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10732727	0.84[ASN][1000 genomes]
rs11162684	0.81[ASN][1000 genomes]
rs11162685	0.81[ASN][1000 genomes]
rs11162686	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs11162695	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162696	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162697	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578751	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11588913	0.81[EUR][1000 genomes]
rs11591000	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12724768	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12726250	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12727530	0.81[EUR][1000 genomes]
rs12732505	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745266	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12749113	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749224	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754109	0.85[EUR][1000 genomes]
rs12760991	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1331709	0.93[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs1331718	0.90[ASN][1000 genomes]
rs1389942	0.85[MEX][hapmap];0.81[TSI][hapmap]
rs1389947	0.81[EUR][1000 genomes]
rs1412129	0.86[ASN][1000 genomes]
rs1412131	0.84[ASN][1000 genomes]
rs1412134	0.82[ASN][1000 genomes]
rs1412137	0.81[ASN][1000 genomes]
rs1494843	0.85[EUR][1000 genomes]
rs1494852	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1494856	0.81[EUR][1000 genomes]
rs1494865	0.90[EUR][1000 genomes]
rs17417360	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17418410	0.85[EUR][1000 genomes]
rs17418579	0.81[EUR][1000 genomes]
rs17451181	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17451905	0.90[EUR][1000 genomes]
rs17453037	0.80[EUR][1000 genomes]
rs1888766	0.86[ASN][1000 genomes]
rs1929622	0.82[ASN][1000 genomes]
rs2132055	0.85[EUR][1000 genomes]
rs2882993	0.81[ASN][1000 genomes]
rs2934867	0.84[EUR][1000 genomes]
rs3000133	0.84[AMR][1000 genomes]
rs3000178	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3015025	0.84[AMR][1000 genomes]
rs3015098	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3015108	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3015120	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3015124	0.91[ASN][1000 genomes]
rs3015126	0.91[ASN][1000 genomes]
rs33944981	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34146004	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34322872	0.84[EUR][1000 genomes]
rs34510598	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34554398	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35352017	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35490451	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35676104	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35706038	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35707904	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35733452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963120	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36033983	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4414002	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604653	0.85[EUR][1000 genomes]
rs4630085	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012068	0.81[ASN][1000 genomes]
rs58635031	0.84[EUR][1000 genomes]
rs61031256	0.84[EUR][1000 genomes]
rs61767574	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66530141	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6661645	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692670	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6699018	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7516261	0.85[EUR][1000 genomes]
rs7527570	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7536196	0.93[EUR][1000 genomes]
rs7536365	0.93[EUR][1000 genomes]
rs7546200	0.81[ASN][1000 genomes]
rs7555044	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830337	chr1:79791879-79913241	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv546633	chr1:79794719-79877035	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv871649	chr1:79807447-79924175	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv462150	chr1:79835066-79873161	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv546634	chr1:79835066-79873161	Weak transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv462161	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv462173	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv470721	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv546635	chr1:79835066-79877035	Enhancers Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12734357	USP33	cis	cerebellum	SCAN
rs12734357	IFI44L	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79839000-79840600	Enhancers	Fetal Brain Male	brain
2	chr1:79839200-79839800	Enhancers	Adipose Nuclei	Adipose
3	chr1:79839200-79840400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:79839200-79840600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:79839200-79840800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:79839400-79839800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:79839400-79840000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:79839400-79840800	Enhancers	Brain Germinal Matrix	brain
9	chr1:79839600-79840400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:79839600-79842800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links