Variant report

Variant	rs12038879
Chromosome Location	chr1:113922029-113922030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10458458	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs10458459	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs10494160	0.85[ASN][1000 genomes]
rs10857991	0.82[ASN][1000 genomes]
rs10857994	0.86[CHB][hapmap]
rs11102627	0.84[CHB][hapmap]
rs11102628	0.84[CHB][hapmap]
rs11102630	0.85[CHB][hapmap]
rs11102637	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs11102638	0.93[CEU][hapmap]
rs11102639	0.84[CHB][hapmap]
rs11102641	0.94[CEU][hapmap];0.85[CHB][hapmap]
rs11102647	0.84[CHB][hapmap]
rs1112085	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1112543	0.93[CEU][hapmap];0.84[CHB][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];0.84[CHB][hapmap]
rs12022849	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs12023641	0.86[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12024139	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs12026682	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs12027464	0.85[ASN][1000 genomes]
rs12028292	0.85[ASN][1000 genomes]
rs12028450	0.82[ASN][1000 genomes]
rs12030900	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs12031201	0.85[ASN][1000 genomes]
rs12032132	0.85[ASN][1000 genomes]
rs12032137	0.85[ASN][1000 genomes]
rs12032395	0.94[CEU][hapmap];0.85[CHB][hapmap]
rs12032749	0.85[ASN][1000 genomes]
rs12033092	0.95[CHB][hapmap];0.96[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];0.84[CHB][hapmap]
rs12039603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039669	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs12039944	0.93[CEU][hapmap]
rs12044485	0.81[CHB][hapmap]
rs12045148	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs12045559	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs12046451	0.94[CEU][hapmap];0.86[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1539411	0.93[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1573996	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs17013288	0.85[ASN][1000 genomes]
rs17031447	0.85[ASN][1000 genomes]
rs17031448	0.85[ASN][1000 genomes]
rs1936927	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs1936928	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs2027537	0.94[CEU][hapmap];0.86[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];0.84[CHB][hapmap]
rs4839316	0.85[ASN][1000 genomes]
rs4839317	0.85[ASN][1000 genomes]
rs4839320	0.93[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4839323	0.84[CHB][hapmap]
rs4839324	0.93[CEU][hapmap];0.84[CHB][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	0.84[CHB][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

No data

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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