High-density single-nucleotide polymorphism maps of the human genome

Abstract

Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency ≥10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. PuiYan Kwok,

Association of LACC1, CEBPB-PTPN1, RIPK2 and ADO-EGR2 with ocular Behcet’s disease in a Chinese Han population

“…Even within a continent, populations may differ genetically, whereby Japanese and Chinese, differ by 6.78%. 35 Similarly, we did not confirm an association with the other two SNPs (rs1509966 and rs7075773) in ADO-EGR2 and BD susceptibility. Although they had a relatively high statistic power of 0.641 and 0.738, respectively, we could not exclude a false-negative disease association of rs1509966 and rs7075773 in our study.…”

Association of LACC1, CEBPB-PTPN1, RIPK2 and ADO-EGR2 with ocular Behcet’s disease in a Chinese Han population

“…Even within a continent, populations may differ genetically, whereby Japanese and Chinese, differ by 6.78%. 35 Similarly, we did not confirm an association with the other two SNPs (rs1509966 and rs7075773) in ADO-EGR2 and BD susceptibility. Although they had a relatively high statistic power of 0.641 and 0.738, respectively, we could not exclude a false-negative disease association of rs1509966 and rs7075773 in our study.…”

Beyond the “Dominant” and “Recessive” Patterns of Inheritance

“…All of these findings appear to align with "The Edge of Chaos" principle in the origin of oscillations in biological systems, explaining complex phenomena [33,34]. Regarding the X chromosome, it is known that the evolutionary dynamics of SNPs on the X chromosome differ from those on autosomes [35]. XLD diseases were primarily found in CGI+ X-linked genes, which are not susceptible to methylation.…”

Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19

“…Several of the detected SNPs show a high frequency within the patient material ( table 1 ). However, a considerable number of variations (30 out of 73) show frequencies of less than 1% and the prevalence of these “private” or rare variations is high, compared to previous estimates of 7% [21] .…”

Association of LACC1, CEBPB-PTPN1, RIPK2 and ADO-EGR2 with ocular Behcet’s disease in a Chinese Han population

“…Even within a continent, populations may differ genetically, whereby Japanese and Chinese, differ by 6.78%. 35 Similarly, we did not confirm an association with the other two SNPs (rs1509966 and rs7075773) in ADO-EGR2 and BD susceptibility. Although they had a relatively high statistic power of 0.641 and 0.738, respectively, we could not exclude a false-negative disease association of rs1509966 and rs7075773 in our study.…”

Beyond the “Dominant” and “Recessive” Patterns of Inheritance

“…All of these findings appear to align with "The Edge of Chaos" principle in the origin of oscillations in biological systems, explaining complex phenomena [33,34]. Regarding the X chromosome, it is known that the evolutionary dynamics of SNPs on the X chromosome differ from those on autosomes [35]. XLD diseases were primarily found in CGI+ X-linked genes, which are not susceptible to methylation.…”

Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19

“…Several of the detected SNPs show a high frequency within the patient material ( table 1 ). However, a considerable number of variations (30 out of 73) show frequencies of less than 1% and the prevalence of these “private” or rare variations is high, compared to previous estimates of 7% [21] .…”

Association of LACC1, CEBPB-PTPN1, RIPK2 and ADO-EGR2 with ocular Behcet’s disease in a Chinese Han population

“…Even within a continent, populations may differ genetically, whereby Japanese and Chinese, differ by 6.78%. 35 Similarly, we did not confirm an association with the other two SNPs (rs1509966 and rs7075773) in ADO-EGR2 and BD susceptibility. Although they had a relatively high statistic power of 0.641 and 0.738, respectively, we could not exclude a false-negative disease association of rs1509966 and rs7075773 in our study.…”

Beyond the “Dominant” and “Recessive” Patterns of Inheritance

“…All of these findings appear to align with "The Edge of Chaos" principle in the origin of oscillations in biological systems, explaining complex phenomena [33,34]. Regarding the X chromosome, it is known that the evolutionary dynamics of SNPs on the X chromosome differ from those on autosomes [35]. XLD diseases were primarily found in CGI+ X-linked genes, which are not susceptible to methylation.…”

Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19

“…Several of the detected SNPs show a high frequency within the patient material ( table 1 ). However, a considerable number of variations (30 out of 73) show frequencies of less than 1% and the prevalence of these “private” or rare variations is high, compared to previous estimates of 7% [21] .…”