PMC:5985360 / 10068-12086 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5985360","sourcedb":"PMC","sourceid":"5985360","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5985360","text":"We mapped 15 restriction sites, including the seven canonical sites, to the reference human genome sequence. We identified 12 known markers that predict the presence or absence of ten of these sites. Of the canonical sites, we predicted 5′ ε HincII with rs3834466, Gγ1 HindIII with rs2070972, Aγ1 HindIII with rs28440105, and 3′ ψβ HincII with rs968857 (Table 1); similar results were described in a previously reported analysis of rs3834466, rs28440105, rs10128556, and rs968857.40 Pairwise correlation (measured via r2) between these variants and rs334 was weak to nonexistent (Table 1). On the basis of these four RFLP-predicting markers, we identified ten unique haplotypes. V˜2 between the set of ten haplotypes and rs334 was 0.079 (Figure 1).\nFigure 1 Pairwise Association Plots\nFor each triangle, vertices indicate markers, and edges are labeled with V˜2 association values. The associations on the bottom edges are conditional on the presence of the βS or βA allele.\n(A) Associations between rs334, the RFLP-predicting markers, and the one marker with pairwise r2≥0.4 with rs334.\n(B) Associations between rs334, the RFLP-predicting markers, and the set of three markers with pairwise r2≥0.3 with rs334.\n(C) Associations between rs334, the RFLP-predicting markers, and the set of 27 markers with pairwise r2≥0.2 with rs334.\nTable 1 Molecular Characterization of the Classical Sickle Haplotypes\nSite\n3′ ψβ HincII Aγ1 HindIII Gγ1 HindIII 5′ ε HincII\nSequencea GTTGAC AAGCTT AAGCTT GTTGAC\nRange 5,260,457–5,260,462 5,269,799–5,269,804 5,274,717–5,274,722 5,291,563–5,291,567\nrsID rs968857 rs28440105 rs2070972 rs3834466\nPosition (hg19) 5,260,458 5,269,799 5,274,717 5,291,563–5,291,564\nSenegal + − + −\nBenin + − − −\nCAR − − + −\nCameroon + + + −\nArabian/Indian + − + +\nr2b 0.000 0.016 0.003 0.020\nD′b −0.104 0.930 0.094 −0.853\nAncestral T C C G\nStatus + − − −\nDerived C A A GT\nStatus − + + +\na Underlining indicates the polymorphic position.\nb Pairwise linkage disequilibrium values are shown with respect to rs334.","divisions":[{"label":"figure","span":{"begin":749,"end":1330}},{"label":"label","span":{"begin":749,"end":757}},{"label":"caption","span":{"begin":758,"end":1330}},{"label":"p","span":{"begin":758,"end":784}},{"label":"p","span":{"begin":785,"end":974}},{"label":"p","span":{"begin":975,"end":1087}},{"label":"p","span":{"begin":1088,"end":1210}},{"label":"p","span":{"begin":1211,"end":1330}},{"label":"label","span":{"begin":1331,"end":1338}},{"label":"caption","span":{"begin":1339,"end":1400}},{"label":"p","span":{"begin":1339,"end":1400}},{"label":"table","span":{"begin":1401,"end":1894}},{"label":"tr","span":{"begin":1401,"end":1405}},{"label":"th","span":{"begin":1401,"end":1405}},{"label":"tr","span":{"begin":1406,"end":1454}},{"label":"th","span":{"begin":1406,"end":1418}},{"label":"th","span":{"begin":1419,"end":1430}},{"label":"th","span":{"begin":1431,"end":1442}},{"label":"th","span":{"begin":1443,"end":1454}},{"label":"tr","span":{"begin":1455,"end":1492}},{"label":"td","span":{"begin":1455,"end":1464}},{"label":"td","span":{"begin":1465,"end":1471}},{"label":"td","span":{"begin":1472,"end":1478}},{"label":"td","span":{"begin":1479,"end":1485}},{"label":"td","span":{"begin":1486,"end":1492}},{"label":"tr","span":{"begin":1493,"end":1578}},{"label":"td","span":{"begin":1493,"end":1498}},{"label":"td","span":{"begin":1499,"end":1518}},{"label":"td","span":{"begin":1519,"end":1538}},{"label":"td","span":{"begin":1539,"end":1558}},{"label":"td","span":{"begin":1559,"end":1578}},{"label":"tr","span":{"begin":1579,"end":1623}},{"label":"td","span":{"begin":1579,"end":1583}},{"label":"td","span":{"begin":1584,"end":1592}},{"label":"td","span":{"begin":1593,"end":1603}},{"label":"td","span":{"begin":1604,"end":1613}},{"label":"td","span":{"begin":1614,"end":1623}},{"label":"tr","span":{"begin":1624,"end":1689}},{"label":"td","span":{"begin":1624,"end":1639}},{"label":"td","span":{"begin":1640,"end":1649}},{"label":"td","span":{"begin":1650,"end":1659}},{"label":"td","span":{"begin":1660,"end":1669}},{"label":"td","span":{"begin":1670,"end":1689}},{"label":"tr","span":{"begin":1690,"end":1705}},{"label":"td","span":{"begin":1690,"end":1697}},{"label":"td","span":{"begin":1698,"end":1699}},{"label":"td","span":{"begin":1700,"end":1701}},{"label":"td","span":{"begin":1702,"end":1703}},{"label":"td","span":{"begin":1704,"end":1705}},{"label":"tr","span":{"begin":1706,"end":1719}},{"label":"td","span":{"begin":1706,"end":1711}},{"label":"td","span":{"begin":1712,"end":1713}},{"label":"td","span":{"begin":1714,"end":1715}},{"label":"td","span":{"begin":1716,"end":1717}},{"label":"td","span":{"begin":1718,"end":1719}},{"label":"tr","span":{"begin":1720,"end":1731}},{"label":"td","span":{"begin":1720,"end":1723}},{"label":"td","span":{"begin":1724,"end":1725}},{"label":"td","span":{"begin":1726,"end":1727}},{"label":"td","span":{"begin":1728,"end":1729}},{"label":"td","span":{"begin":1730,"end":1731}},{"label":"tr","span":{"begin":1732,"end":1748}},{"label":"td","span":{"begin":1732,"end":1740}},{"label":"td","span":{"begin":1741,"end":1742}},{"label":"td","span":{"begin":1743,"end":1744}},{"label":"td","span":{"begin":1745,"end":1746}},{"label":"td","span":{"begin":1747,"end":1748}},{"label":"tr","span":{"begin":1749,"end":1771}},{"label":"td","span":{"begin":1749,"end":1763}},{"label":"td","span":{"begin":1764,"end":1765}},{"label":"td","span":{"begin":1766,"end":1767}},{"label":"td","span":{"begin":1768,"end":1769}},{"label":"td","span":{"begin":1770,"end":1771}},{"label":"tr","span":{"begin":1772,"end":1799}},{"label":"td","span":{"begin":1772,"end":1775}},{"label":"td","span":{"begin":1776,"end":1781}},{"label":"td","span":{"begin":1782,"end":1787}},{"label":"td","span":{"begin":1788,"end":1793}},{"label":"td","span":{"begin":1794,"end":1799}},{"label":"tr","span":{"begin":1800,"end":1829}},{"label":"td","span":{"begin":1800,"end":1803}},{"label":"td","span":{"begin":1804,"end":1810}},{"label":"td","span":{"begin":1811,"end":1816}},{"label":"td","span":{"begin":1817,"end":1822}},{"label":"td","span":{"begin":1823,"end":1829}},{"label":"tr","span":{"begin":1830,"end":1847}},{"label":"td","span":{"begin":1830,"end":1839}},{"label":"td","span":{"begin":1840,"end":1841}},{"label":"td","span":{"begin":1842,"end":1843}},{"label":"td","span":{"begin":1844,"end":1845}},{"label":"td","span":{"begin":1846,"end":1847}},{"label":"tr","span":{"begin":1848,"end":1862}},{"label":"td","span":{"begin":1848,"end":1854}},{"label":"td","span":{"begin":1855,"end":1856}},{"label":"td","span":{"begin":1857,"end":1858}},{"label":"td","span":{"begin":1859,"end":1860}},{"label":"td","span":{"begin":1861,"end":1862}},{"label":"tr","span":{"begin":1863,"end":1879}},{"label":"td","span":{"begin":1863,"end":1870}},{"label":"td","span":{"begin":1871,"end":1872}},{"label":"td","span":{"begin":1873,"end":1874}},{"label":"td","span":{"begin":1875,"end":1876}},{"label":"td","span":{"begin":1877,"end":1879}},{"label":"tr","span":{"begin":1880,"end":1894}},{"label":"td","span":{"begin":1880,"end":1886}},{"label":"td","span":{"begin":1887,"end":1888}},{"label":"td","span":{"begin":1889,"end":1890}},{"label":"td","span":{"begin":1891,"end":1892}},{"label":"td","span":{"begin":1893,"end":1894}},{"label":"table-wrap-foot","span":{"begin":1895,"end":1944}},{"label":"footnote","span":{"begin":1895,"end":1944}},{"label":"label","span":{"begin":1895,"end":1896}},{"label":"p","span":{"begin":1897,"end":1944}},{"label":"label","span":{"begin":1945,"end":1946}}],"tracks":[{"project":"2_test","denotations":[{"id":"29526279-28800727-2046651","span":{"begin":480,"end":482},"obj":"28800727"}],"attributes":[{"subj":"29526279-28800727-2046651","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#bdec93","default":true}]}]}}