Variant report

Variant	rs12087470
Chromosome Location	chr1:186578830-186578831
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10798051	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911877	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10911878	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10911888	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10911890	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911892	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911895	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10911898	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580808	0.86[EUR][1000 genomes]
rs11582183	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11800288	0.81[ASN][1000 genomes]
rs11800338	0.81[ASN][1000 genomes]
rs11802705	0.80[ASN][1000 genomes]
rs11804161	0.83[ASN][1000 genomes]
rs11804785	0.81[ASN][1000 genomes]
rs11805124	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806329	0.83[ASN][1000 genomes]
rs11806663	0.81[ASN][1000 genomes]
rs11807318	0.83[ASN][1000 genomes]
rs11807443	0.83[ASN][1000 genomes]
rs11807927	0.81[ASN][1000 genomes]
rs11808165	0.81[ASN][1000 genomes]
rs11808900	0.82[JPT][hapmap]
rs11809088	0.81[ASN][1000 genomes]
rs11810534	0.85[JPT][hapmap]
rs11811259	0.81[ASN][1000 genomes]
rs11811260	0.81[ASN][1000 genomes]
rs11811335	0.81[ASN][1000 genomes]
rs12093901	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12402521	1.00[CEU][hapmap]
rs12723621	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12726528	0.83[ASN][1000 genomes]
rs12726764	0.83[ASN][1000 genomes]
rs12728706	0.82[EUR][1000 genomes]
rs12739006	0.81[ASN][1000 genomes]
rs12747991	0.83[ASN][1000 genomes]
rs12750371	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12753223	0.83[ASN][1000 genomes]
rs16825675	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1799957	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs1929092	0.81[EUR][1000 genomes]
rs2024761	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2180167	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2206974	0.81[ASN][1000 genomes]
rs2207727	0.82[EUR][1000 genomes]
rs2223783	0.81[ASN][1000 genomes]
rs2223784	0.81[ASN][1000 genomes]
rs2383508	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2383509	0.81[ASN][1000 genomes]
rs34200789	0.83[ASN][1000 genomes]
rs34272627	0.80[ASN][1000 genomes]
rs34310508	0.81[ASN][1000 genomes]
rs34396375	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34778311	0.81[ASN][1000 genomes]
rs35240980	0.83[ASN][1000 genomes]
rs35481005	0.80[ASN][1000 genomes]
rs35636342	0.81[ASN][1000 genomes]
rs35643079	0.82[EUR][1000 genomes]
rs36016361	0.83[ASN][1000 genomes]
rs36030781	0.83[ASN][1000 genomes]
rs36105782	0.82[EUR][1000 genomes]
rs3844242	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3901950	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4140432	0.83[JPT][hapmap]
rs4140433	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4567244	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs59547074	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6425035	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6425038	0.84[EUR][1000 genomes]
rs6659683	1.00[CEU][hapmap]
rs6666413	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6666813	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672836	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6675505	0.81[EUR][1000 genomes]
rs6677346	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6678198	0.81[ASN][1000 genomes]
rs6680055	0.81[ASN][1000 genomes]
rs6680252	0.83[EUR][1000 genomes]
rs6689065	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689727	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6694957	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71634175	0.81[ASN][1000 genomes]
rs71634176	0.81[ASN][1000 genomes]
rs7518525	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539054	0.85[EUR][1000 genomes]
rs7556360	0.81[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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12087470	C1orf14	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186575600-186587400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:186575800-186579200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:186578200-186579200	Enhancers	Colon Smooth Muscle	Colon
4	chr1:186578400-186579000	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:186578400-186579000	Enhancers	Stomach Smooth Muscle	stomach
6	chr1:186578400-186579600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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