Variant report

Variant	rs12727530
Chromosome Location	chr1:79961748-79961749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10493629	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162686	0.87[CHB][hapmap]
rs11578751	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11588913	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591000	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12724768	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12726250	0.82[EUR][1000 genomes]
rs12727721	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12732505	0.81[EUR][1000 genomes]
rs12734357	0.81[EUR][1000 genomes]
rs12739748	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12739762	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12742448	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12745266	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12749113	0.81[EUR][1000 genomes]
rs12749224	0.81[EUR][1000 genomes]
rs12754109	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12760991	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1331709	0.94[CHB][hapmap]
rs1389940	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1389942	0.89[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs1389943	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1389944	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1389947	0.81[EUR][1000 genomes]
rs1494843	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494852	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1494856	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494857	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1494865	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17417360	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17418410	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17418579	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17451181	0.82[ASN][1000 genomes]
rs17451905	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17453037	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994938	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2132055	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2934867	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2934868	0.80[AMR][1000 genomes]
rs2934871	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3000101	0.83[AMR][1000 genomes]
rs3000142	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3000178	0.80[ASN][1000 genomes]
rs3015013	0.80[AMR][1000 genomes]
rs3015017	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3015019	0.84[AMR][1000 genomes]
rs3015021	0.84[AMR][1000 genomes]
rs3015022	0.83[AMR][1000 genomes]
rs3015108	0.80[ASN][1000 genomes]
rs3015120	0.85[ASN][1000 genomes]
rs34146004	0.81[EUR][1000 genomes]
rs34322872	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34510598	0.81[EUR][1000 genomes]
rs34554398	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34763301	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35352017	0.82[EUR][1000 genomes]
rs35446319	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35490451	0.84[EUR][1000 genomes]
rs35624469	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35676104	0.81[EUR][1000 genomes]
rs35706038	0.82[EUR][1000 genomes]
rs35707904	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35733452	0.81[EUR][1000 genomes]
rs35938583	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35963120	0.82[EUR][1000 genomes]
rs36033983	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4506421	0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4604653	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4630085	0.81[EUR][1000 genomes]
rs58635031	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59395170	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61031256	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61767574	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66530141	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6661645	0.81[EUR][1000 genomes]
rs7516261	0.80[ASN][1000 genomes]
rs7527570	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7536196	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7536365	0.87[EUR][1000 genomes];0.86[ASN][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	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
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12727530	C20orf123	trans	parietal	SCAN
rs12727530	USP33	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79959600-79962200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr1:79960000-79963200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:79960600-79961800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:79960600-79962800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:79960600-79964400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:79961200-79961800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:79961400-79961800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr1:79961400-79961800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:79961600-79961800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:79961600-79962200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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