Variant report

Variant	rs12039603
Chromosome Location	chr1:113922234-113922235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10458458	0.93[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs10458459	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs10494160	0.85[ASN][1000 genomes]
rs10857991	0.82[ASN][1000 genomes]
rs10857994	0.81[CHB][hapmap]
rs11102627	0.81[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs11102628	0.81[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs11102637	0.93[CEU][hapmap]
rs11102638	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs11102639	0.81[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs11102641	0.93[CEU][hapmap];0.80[CHB][hapmap]
rs11102647	0.81[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs1112085	0.93[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1112543	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12021783	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12022213	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12022849	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12023641	0.86[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12024139	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs12026682	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12027464	0.85[ASN][1000 genomes]
rs12028292	0.85[ASN][1000 genomes]
rs12028450	0.82[ASN][1000 genomes]
rs12030900	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12031069	0.83[JPT][hapmap]
rs12031201	0.85[ASN][1000 genomes]
rs12032132	0.85[ASN][1000 genomes]
rs12032137	0.85[ASN][1000 genomes]
rs12032395	0.93[CEU][hapmap];0.83[CHB][hapmap]
rs12032749	0.85[ASN][1000 genomes]
rs12033092	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12033935	0.85[ASN][1000 genomes]
rs12033996	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12034394	0.85[ASN][1000 genomes]
rs12034896	0.85[ASN][1000 genomes]
rs12035230	0.85[ASN][1000 genomes]
rs12036205	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12036995	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12037686	0.85[ASN][1000 genomes]
rs12038473	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs12038879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039669	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs12039944	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs12045148	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs12045559	0.93[CEU][hapmap]
rs12046451	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs12048327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12049093	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12049447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567622	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12568854	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1418607	0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1539411	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1573996	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs17013288	0.85[ASN][1000 genomes]
rs17031447	0.85[ASN][1000 genomes]
rs17031448	0.85[ASN][1000 genomes]
rs1936927	0.93[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs1936928	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs2027537	0.93[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35862767	0.84[ASN][1000 genomes]
rs4838987	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4838988	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4839316	0.85[ASN][1000 genomes]
rs4839317	0.85[ASN][1000 genomes]
rs4839320	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4839323	0.81[CHB][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap]
rs4839324	0.93[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap]
rs55737954	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66565865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665552	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6688827	0.81[CHB][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]

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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1012143	chr1:113861524-113930779	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12039603	PHTF1	cis	cerebellum	SCAN
rs12039603	CAPZA1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113918800-113931200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:113918800-113931200	Weak transcription	Right Atrium	heart

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