Variant report

Variant	rs12772884
Chromosome Location	chr10:96700630-96700631
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10882498	0.81[ASN][1000 genomes]
rs11188093	0.81[ASN][1000 genomes]
rs11188105	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11498525	0.81[ASN][1000 genomes]
rs11595422	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200313	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12772675	0.94[ASN][1000 genomes]
rs1322181	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1341163	0.80[MEX][hapmap]
rs1505	0.89[ASN][1000 genomes]
rs1555474	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1853208	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1856908	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs1891071	0.80[MEX][hapmap]
rs1934960	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1934964	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934965	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934969	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1934985	0.80[MEX][hapmap]
rs1998321	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096069	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2104161	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2104162	0.81[ASN][1000 genomes]
rs2253635	0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275620	0.80[MEX][hapmap]
rs2860906	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35013847	0.82[ASN][1000 genomes]
rs35687798	0.94[ASN][1000 genomes]
rs3740504	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4110516	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4362080	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4466755	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4608002	0.81[ASN][1000 genomes]
rs4617515	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4638239	0.81[EUR][1000 genomes]
rs4917623	0.95[JPT][hapmap]
rs4917641	0.94[ASN][1000 genomes]
rs4918758	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4918766	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6583963	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6583964	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7073165	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079343	0.80[ASN][1000 genomes]
rs7083767	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7084717	0.81[ASN][1000 genomes]
rs7475054	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7895963	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7903917	0.89[ASN][1000 genomes]
rs7910936	0.80[MEX][hapmap]
rs7912502	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7915414	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7916649	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3336672	chr10:96543010-96711519	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1037973	chr10:96563228-96711744	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1047782	chr10:96581094-96718479	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv551962	chr10:96680265-96734339	Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12772884	PPP1R3C	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96698600-96702000	Weak transcription	Fetal Intestine Large	intestine
2	chr10:96699200-96702800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:96699600-96701600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:96700600-96700800	Flanking Active TSS	Liver	Liver

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