Supplemental Table S1. Sequences of primer sets and their position on the X chromosome (UCSC Genome browser March 2006 hg18) ID forward (5'-3') reverse (5'-3') position on X NXF5 5'-GCACACAAAATGTCCACGAAA 5'-ACCAGGATGGAGGTGAAGTCA 100979240 RP11-533H4 5'-TTCCCCAGCAACCTATCAAAA 5'-TTCTTTGGTAGCAACACATGCTTT 149069153 GPR50 5'-CGATATGCTGGTGGCCATCT 5'-CAGCCCCCAATGGACATG 150098932 RP11-157E12bis 5'-CCATGGCACAAATGCAGATG 5'-CAAGAGTTGTCTCCTCCTGTTTCA 151286389 RP11-473F11 5'-TGTGGCATTGTCAGGAACACTAC 5'-GCCTGGCTCCTTGTTATGCT 151479521 GABRQ 5'-CTCGCGGAGGGCAACTA 5'-CAGCAGAGGAGAACTCGAAGTG 151557409 RP11-76K17 5'-CACGGCCACAGGAACTCAT 5'-TTCCTCTTGCCTTTTGTGGAA 151986362 TREX-prox 5'-CTTCTGCTGCGGCTTTCAG 5'-GCCATAACATTTCCAGTTTGTCTTT 152359210 66N11 5'-GAGGGTGACGGGAATATCCT 5'-TGGTGGCTGAGCGGAAA 152529125 L36PROX2 5'-CAACCAGCAAGTAGGAGGAAGAC 5'-GAGTTCATACTGACCCATCCAATTT 152534029 L36PROX 5'-GGCATGTAGGCTGCTCCAA 5'-CAGCCCCTTAGGAGGTTGCT 152547057 U52111 5'-ACTGCTCTGATGCGGAATCC 5'-TGTGGCACCCTCCGAATC 152568064 PNCK 5'-CGAGTGCCGGTTTCTTCTG 5'-TGGGTCTGGGAGCAATGAG 152586864 PNCK-3' 5'-AAACTGGAGGCCAGAAGGAAA 5'-CCCGCTGGCTCGTCTTT 152594059 SLC6A8 5'-GCTGGTCAGATTTGTGCTTCAG 5'-CCAGACCCCAAACTGCATTC 152604452 T33PROX 5'-TGAGCTGGTCATTCTCCTCCATGTA 5'-GCCTCCAATGAAGCCTTTAAAA 152622668 ABCD-5' 5'-TCTCCTCCCTTTGGAAATTGG 5'-GGATTTGCAGAGTGGGAGAGAT 152632256 ABCD2 5'-TCAACACCCCGGACACAAA 5'-GACCTTCAGAGTCCAGCTCACA 152636303 ABCD3 5'-GCTATGGACAGCAGTCTTATCTCAGA 5'-GACATGGCAGGAGGAGCATT 152639552 ABCD4 5'-GCCATATGTCCCCCTAGAACTT 5'-CAGTAGTTGACAAAGCCTTCATTC 152640214 T88PROX3 5'-AGGGAATGGCAGGACTTCACT 5'-CCTGGAGCAGGGCCTCTAA 152638727 T88PROX 5'-GAAGGGTTGGCAATAACAAACAC 5'-CGATGGAACAGGTAGAACCTGTCT 152641635 T88PROX2 5'-TCTGCTTCCTCTCCTCCTCAAG 5'-AGGAGCTCTCGAGGCTCAAAC 152645069 T88PROX4 5'-CTTATACCCCCTTACACCTTGAGTTT 5'-GGCCGAGAGCCAGAGGTT 152647701 ABCD1 5'-GAAGGCAGCCTTGGAAAAGA 5'-GGGCAATAGTGAAGGCTTCTGT 152654784 ABCD1-pro-repeat 5'-CGTACGGTGGTGTGCTCTACA 5'-TCCTTACCTCTGCGGGATGT 152658837 ABCD1-post-repeat 5'-GATGGTCCCAAGGAGCCAAT 5'-GGGAAAGGCAGGTTAGGTTAGAG 152669132 PLXNB3-5' 5'-CCAAGGAAAGGCTAGGACTAACTG 5'-TTAGATGAATCATCCCCACTGACA 152676816 ABCD1-3' 5'-GGGTCAAGTGCCCCAAACT 5'-GGCGGAAGTGGCCATTC 152702093 314B3 5'-TGGTGGATGGAAGAACATTCAC 5'-CGGCAAGGGCTTCCTCTTA 152750672 314B3bis 5'-GGAGCCTTGGCCTGGAGTA 5'-AAAGCAGCAAACTCAGCTCATG 152753287 PDZK4-3' 5'-ACCCAGGTGCTCTGCTGTCT 5'-TGCAAAATGCAGGATACTGGTT 152755120 PDZK4 5'-AAGCTTCGAGAGCATCGTGAA 5'-TCGTGGAAAGCTTGAGTTGTGT 152762310 S49PROX2 5'-CACCTCAGGTTAGCACTATTGCAA 5'-TTTGGCTTTACTGCAATTTCTCAT 152768128 S49PROX 5'-CACCCCTGATTCTCTTGTTCCT 5'-GGACATTGGAAGAGGGATTGTC 152769938 L1CAM 5'-TTCGTTCATTGGCCAGTACAGT 5'-TGGCCCCTGAGCTGTCA 152781386 L1CAM5 5'-CCGCCCAAGCCAGAAC 5'-AGAGGGCCCCAACTTTAA 152781819 L1CAM6 5'-CCTCTCAACCCAAGTCTTCCA 5'-GAGGTAAAGCGACAGGATGGT 152783362 L1CAM7 5'-TGAGGGTGGTAGAGGTCTGGTT 5'-GGAAATGGCGCCTGAAAA 152785235 L1CAM8 5'-CAAGACCTTTCCCCTCTTACATC 5'-CCCTTCGCCCCATCTCA 152787094 L1CAM-3' 5'-GGTGAGCACATTGGCAAAG 5'-GACGAGCGGGTGACGAT 152789491 L1CAMtris 5'-CTTCCATCATCCTGACACAGAA 5'-CTCCCCACCCCTCCAGTT 152789319 L1CAMquis 5'-GCGCCGTGGAGACTGTT 5'-CGCTCTCTCCACCCTGTCTT 152790432 L1CAMbis 5'-GACCCCACCCATTCAGGAT 5'-AATTGGATTAGGAGGGAAGCA 152792185 L1CAM-ex1-int1 5'-CCAACATAGCGGCGAAGGTA 5'-AGATCCCCGAGGAATGTGAGT 152794279 ARHGAP4-5' 5'-TGTGCCTGTTGGTGTGTATACG 5'-GGGAGCCTTAAAGGGACACAGT 152799141 Q71F78-5' 5'-TGGATTGTAGTGCGTGTTCTTTG 5'-CTCCATTCCAGGTCAGACTTTTG 152803646 Q71F78bis 5'-GGCCAAGAGGGCGTACTT 5'-TCAGCAAAGGCAGGAAGCT 152806102 Q71F78 5'-CCCACAAGGTGGGAGTGA 5'-TGACCAAGAGCAGAGCATCTG 152809602 AVPR2 5'-GAGCCCAGGTCCTTCCATCT 5'-TCCATTCACCAAACTGCAAGTG 152820717 ARHGAP4 5'-ACCCAGCAGCCACTGATCA 5'-GGAGGCAGCTGAGGAAGGA 152826013 HCFC1-prox 5'-GGTGTCACCAAAATAAGGGTATCAA 5'-TGCCCAGTGCTCTGTTTCC 152836397 HCFC1-5' 5'-CTCACCCTGTGTAGTCACCTCAAG 5'-TGCTCCAGTCCTCCTTTGGA 152843727 HCFC1 5'-TGTGCGCGCCAAAGG 5'-GAACTGTCACCATCTGAGATTTTTTC 152868681 ITBA1 5'-GGGCCTCTCATCATGTCTTCA 5'-ACAGCAGTGTCCACGTCTTCTC 152913063 MECP2 5'-TGCTGGATGAATAACCACAACAC 5'-GAAGGTCTCCAGCCATCAGAAG 152958370 MECP2-5' 5'-TCCCAGCTGAGAGTCCATCTG 5'-CACGTCTTCTCAACCTAATGGAATT 153056400 OPN1LW 5'-GGCCCGTTGGTTGGAAAC 5'-GGGCACGGATGACCTGTTAG 153061997 TKTL1 5'-GGTGGCGGGAGAATGTCA 5'-CTCCCCGCTAAAATGAAAACC 153177801 Z49258 5'-GGATGGGACGCTGCTACAGA 5'-GGACATGGTATCAGGTGGACTCA 153190721 Z1 5'-CGTCCCAGGCCCTCTGT 5'-CCCCGATGAAAAAGATGTCA 153193131 Z2 5'-AATGGCCCACTGGACACA 5'-GTCCTTTTGCTTTCATAAATGGA 153196063 Z3 5'-GGGCAGTAGATCAGTCAGTCATT 5'-CGAATATGTAGTTTAGAAAACTGCATTTAG 153198651 Z6 5'-TGGGCCACTGCCACACT 5'-GACTTGGCCCCTGATCTCA 153200762 Z7 5'-AGGAGGGCAGGCAAGAGA 5'-CAGACGGCGCCCTCAA 153201198 Z4 5'-GGCAGAGTCATGGAGCCTTT 5'-GATGCTGTTCACCCTCAGTTAGA 153201878 Z5 5'-ATATAGCCATGTTCCGAACCAT 5'-CGTGGAGACGGCATCAGT 153203925 T88DIST 5'-GCCATAAAGCAGGTGTTTCCA 5'-TTTCCATTTGGTGGCGTTTT 153207901 Z49258bis 5'-CACAGCAAATGCAGAAAACAGT 5'-TTTCCAGGCGCAAACACT 153209975 TKTL1-3' 5'-GAATTCCCTTCGCTGTTTGC 5'-TTTCGCTGCTGCCTGACA 153211549 T88DIST2 5'-GGCCGAGGTCAGGGTTAGAG 5'-ACGGAATGACACATCAGATCATTC 153214253 EDMD-5' 5'-CCGCGGGTCGCACTTAC 5'-CAAATCAGTGGCTCTCCCTCTT 153232487 EDMD 5'-CATGCACGCTACCAGCAGTC 5'-AGAATGATGTGCCAGAGACGC 153263150 RPL10-5' 5'-CCCCAGACAGGTCCAAAAGA 5'-AGGGTCAAGGCAAATGTCCTT 153265997 RPL10-5'-repeat 5'-CGGTGCACACGCAACAGT 5'-GGGAATGGAACGCTTAGAGAAG 153271579 RPL10-5'-post-repeat 5'-TTGTACTGCCCCAGTGGTGTT 5'-GATGCCGGCGGTGACTT 153278517 RPL10 5'-GCAGACAGACCGCCTATATAAGC 5'-CACCACACCGAAGGGAAAGA 153279701 ATP6AP1 5'-GCGTGTACCGTTCAGCCCTAT 5'-GTCAGCAGAGCAGGAACCTCTAG 153294001 TAZ-5' 5'-TCAGAAGGAAGGAGGTTTGCA 5'-CATTGGAGATAACCCTGAGACCAT 153299985 TAZ 5'-CAGTGAAGCTCCAGTGAAAACCT 5'-AACCCCCAAGTGGCCATT 153308818 TAZ-3' 5'-GCTCTCCTTGTTGACCCTCAGA 5'-ATGGGACATCTTCGGACTTGA 153315050 GDI-A 5'-TGCCCGGCACTGGTTTAC 5'-TAGGCGACGGAGCCATTG 153316098 GDI-B 5'-GAGCCCTTCCCGTGC 5'-GACAGCACAGAGAAAGTGACCAA 153321999 GDI1 5'-CCTGCAACGACATCAAAGACA 5'-TTTGCGCTTCATGTTCTCAAG 153324032 FAM50A-5' 5'-CCAAGGAGCTGCAGATGTG 5'-CGTAAGCACTAGCTCCATGTTG 153327376 FAM50A-prox 5'-GAAAGGGCAACACCATGCA 5'-TCACTGAAGTCTTTCCGAAGGAT 153330718 FAM50A1 5'-CAAGACGCCGCTTTCCT 5'-GTGACGATGAAGTCGTAGAAGCT 153330705 FAM50A2 5'-CAGGCTCTCATGTGCTTTCTG 5'-TCCCCAGGCACGTATGAC 153331699 FAM50A3 5'-GGCAAATGTGGAGATCTGATG 5'-GGCCACGCTGAATGAGACA 153332321 FAM50A4 5'-TAAGGTCACCAAGGATCAGTGTGT 5'-ACAGCCCCCAGGAACGA 153332919 FAM50A 5'-ACTGTCCAGCAGAAGCCATGT 5'-TTGCAGGAACTGGCTTCCAT 153334113 FAM50A5 5'-CCCCTTTGTGTTATACAGTGCAA 5'-TCGTGTCTAAAAAACACCATCAA 153335131 FAM50A6 5'-TTTCTGCTTCTCCAGGAAACC 5'-TGGGCCTCATCCATTTAGTTG 153337320 FAM50A-3' 5'-TTGTGCCCCGCATGGT 5'-TGCGACAAAGGGTCCTCTT 153340039 PLXNA3 5'-CGCAGGGAAGGGTTTGTG 5'-AAAAGAGGGTCCCAGGAACAG 153344426 T33DIST3 5'-GACATGCCAAGTGATCAACGA 5'-GGGCCGCCCAAGAAAG 153348735 PLXNA3bis 5'-GCATTGGTGCCCAAACAA 5'-GCGGGTGAAGGTGAAGGA 153351225 T33DIST2 5'-GGACTCCTCTCCCCCAGATT 5'-CGCAACTTATGCTTCCGACAA 153354103 T33DIST 5'-CAAGGGTTTGATGTGTGGATGA 5'-TGATCCCTGGAGGCTAAACAA 153374285 FAM3A 5'-GACCCCATAGCCTTGCATGA 5'-TCCTTGTCCTCCAGCCACTT 153394535 G6PD 5'-ACGGACGTCATCTGAGTTGGT 5'-CACCTACTGCAGATGCTGTGTCT 153415030 RP5-865E18 5'-TGGGTGGTGCCAGCATCT 5'-CAGCTTTCCGCCAGTTCCT 153485596 GAB3 5'-GGAGTAAGATTCTGCCACCATTG 5'-CCATCTTGTTCCAGCCTCTGA 153559256 115M6 5'-CCAAATGCCGTGCCTCTTT 5'-TGGACCACGTTGGGTATTCA 153634737 FA8 5'-CCAGACTCCCAGCCAATCC 5'-CAGTGACAGGAAGCATTGAAAGC 153861483 273L24-1 5'-GTGCGCCTCAGGCTTCTC 5'-TGACCAGCCACTTGCCAAT 153934083 273L24-2 5'-GTTGTCTTCAGGCTTCCTTTCC 5'-TGGATCCCCAGAGTTTACAAGAA 153998329 p-F8-T88-1 5'-GTGTTTGACGGTTTCCATGGT 5'-TAGTTGATGACATGTTAGTTGCTTGAA 153998538 p-F8-T88-2 5'-CCCATTAGGAGGTTATGGTGGTT 5'-GCCACGAAAGGGTTCCTTTC 154001098 p-F8-T88-3 5'-TGGCCTCTTCCGCTCTGA 5'-GCAGACCAGGAGCTCATTTTATC 154008127 p-F8-T88-4 5'-AGTCAAGGCAGGATATGTGCAA 5'-TGGAGCCAAGCCAGTTAAATATTT 154009214 p-F8-T88-5 5'-TCCCATAACTGGTGCAGCAA 5'-TCCTTGTTCCCTGCACCAA 154009812 p-F8-T88-7 5'-CACGAAATGAGGGAAAAGTTGTAGT 5'-TCAAGCCGTGGACATACACTCT 154015827 p-F8-T88-8 5'-AGTGCGTGGTACCTGCCTTCT 5'-AGCTCGGGCTCTGCAAGA 154018296 p-F8-T88-9 5'-CCAGGCTTCTTAGAAAGGTCTCAT 5'-AGAAGACTCGCTGAATGTTACAATTTAT 154019224 p-F8-T88-10 5'-AGCGGAGAACATTGAGACACATT 5'-CATGATGTGAGAAGTGGATTTGC 154021938 RP11-143H17 5'-CAAAAGCAATCTTACAAGGACTTCTG 5'-TTTCTGGTGGGAGGGTAAGCT 154025656 228J13 5'-GAGGCCGTGTTTGTGGTAAGA 5'-GGCAGTCCAAGGCCTCAAG 154098032 CLIC2-2 5'-TGCAGTTATTATAACTGGAAAACTTACCTT 5'-CGGCCCGGCACTCAA 154216847 p-F8-K9228-1 5'-TCACTCCAAAGGCAATCAATGA 5'-TGTGCTGCCAATCTCAGTGAA 154218294 p-F8-K9228-3 5'-GCATTGAAAGTGGATCTTACCTGTT 5'-GTGTGTCGGTGAGAGTGTTTCC 154225257 TMLH-2 5'-CACCCCACCTCAGCTTGGT 5'-GCCAAAGGTCATGGAAGCA 154230915 Before-dBP-F8-T88 5'-AACCCCTGACTGTAAGTCTGACAAA 5'-CCTGCAGCTCATCAGAACCA 154243012 405N23 5'-CAGAGAAAATTGCCAGGACAGA 5'-ACCAAATCAAGAAAATGTGTGAGAAT 154304480 95M2 5'-TGCTTTTTCAGGCTCTTTTTAAGC 5'-TGCGATATCATGGCATGCA 154317364 Before-dBP-F8-T88 5'-AACCCCTGACTGTAAGTCTGACAAA 5'-CCTGCAGCTCATCAGAACCA 154363524 TMLH-2 5'-CACCCCACCTCAGCTTGGT 5'-GCCAAAGGTCATGGAAGCA 154375630 p-F8-K9228-3 5'-GCATTGAAAGTGGATCTTACCTGTT 5'-GTGTGTCGGTGAGAGTGTTTCC 154381266 TMLH-1 5'-TTCCTCCTCTCCAACTTCTTGTAAA 5'-TCATGCAAACACAGCTGCTTT 154392836 Before-dBP-F8-K9228 5'-CCAATGGACAGCTAAAGGAAGTAAG 5'-GCTGAAGGGAGGAGTCATATATCC 154428009 After-dBP-F8-K9228 5'-GCGCATCAACTCTCAAAAGGT 5'-GCCTCACCCAACTGTCTTTCTG 154433840 p-F8-K9228-1 5'-TCACTCCAAAGGCAATCAATGA 5'-TGTGCTGCCAATCTCAGTGAA 154493737 RP11-954J6 5'-GCAGAGTGGGCAGAATTCCA 5'-GGCAAAAGGCGGGTGAA 154495676 AR (X-inactiv) 5'-TCCAGAATCTGTTCCAGAGCGTGC 5'-CTGGGACGCAACCTCTCTC 66681781 DXS8087 5'-AAGGCCAGCAGCATCA 5'-GGAGTCCCTGAGGCAG 152547564 rs4898460 5'-TGACGGATGGCTAAACTCAG 5'-CCCAGTCTTCCTTACCATTC 152832742 rs5987215 5'-ATCCAGACCAAATGGAGAGAGT 5'-TCCCGAGTAGCTGGACTACAG 153053456