Haplotype Structure, LD Blocks, and Uneven Recombination Within the LRP5 Gene

Table 1.

SNPs Identified From the C11orf24–LRP5–C22orf23Region, Showing the Method of Identification, Method of Genotyping, and Allele Frequency in 192 UK Individuals

SNP name Method of identification dbSNP ss # Typing method Frequency
C11orf24 c.598G→A ○ 6905350 Invader/RFLP(PstI) 0.49
EO864-6688 ○ 6905352 RFLP/DraI 0.49
EO864-4419G→A ○ 6905353 RFLP/NcoI 0.29
LRP5 g.-14447C→A graphic 6905427 RFLP/DpnII 0.009
LRP5 g.-14279A→G ♦ 6905354 Invader/cRFLP(NruI) 0.34
LRP5 g.-13901G→A graphic 6905428 RFLP/HaeIII 0.06
LRP5 g.-13340-13366del-ins graphic 6905429 Length polymorphism 0.13
LRP5 g.-11215T→A ○ 6905355 NT
LRP5 g.-11094G→A ○ 6905356 NT
LRP5 g.-10088G→A ○ 6905357 Invader/RFLP(FauI) 0.27
LRP5 g.-9693G→A ○ 6905358 Invader 0.27
LRP5 g.-9003T→C ♦ 6905359 NT
LRP5 g.-8870G→A ♦ 6905360 NT
LRP5 g.-5977C→T ♦ 6905361 NT
LRP5 g.-5880T→C ♦ 6905362 NT
LRP5 g.-5802G→C ○ 6905363 Invader/RFLP(HincII) 0.27
LRP5 g.-5677C→T ○ 6905364 Invader/RFLP(MspI) 0.27
LRP5 g.-5264G→A ○ 6905365 Invader/RFLP(AflIII) 0.27
LRP5 g.-4317G→A graphic 6905430 Invader 0.20
LRP5 g.-2945C→T graphic 6905431 Invader 0.20
LRP5 g.-2713C→A graphic 6905432 Invader 0.10
LRP5 g.-2517A→G graphic 6905433 Invader 0.06
LRP5 g.-2366C→G graphic 6905434 Invader 0.08
LRP5 g.-1792T→G graphic 6905435 Invader 0.10
LRP5 g.-864A→G ○ 6905366 Invader/RFLP(MspI) 0.27
LRP5 g.817C→T graphic 6905436 Invader 0.064
LRP5 g.2221C→T ○ 6905367 Invader/cRFLP(Hph) 0.27
LRP5 g.3103C→G ○ 6905368 Invader/RFLP(pflMI) 0.27
LRP5 g.4780G→C ○ 6905369 Invader/RFLP(EcoNI) 0.34
LRP5 g.5151C→T graphic 6905437 Invader 0.075
LRP5 g.5257T→G ○ 6905370 Invader/cRFLP(SnaBI) 0.28
LRP5 g.6088T→C ♦ 6905371 NT
LRP5 g.7374G→A ○ 6905372 Invader/RFLP(AvaI) 0.35
LRP5 g.8003A→G ○ 6905373 NT
LRP5 g.8651T→G ○ 6905374 NT
LRP5 g.8924T→C ○ 6905375 NT
LRP5 g.10133insT ○ 6905376 NT
LRP5 g.10655A→T ○ 6905377 NT
LRP5 g.10674C→T ○ 6905378 NT
LRP5 g.11084T→C ○ 6905379 NT
LRP5 g.11263A→G ○ 6905380 NT
LRP5 g.11386A→G ○ 6905381 NT
LRP5 g.11886A→G ♦ 6905382 NT
LRP5 g.13279C→T ○ 6905383 Invader/PvuII 0.35
LRP5 g.13963C→T ♦ 6905384 Invader 0.006
LRP5 g.14250G→A ○ 6905385 NT
LRP5 g.14560C→T ○ 6905386 NT
LRP5 g.15531delG ○ 6905387 NT
LRP5 g.16868G→A ○ 6905388 NT
LRP5 g.17646G→T ○ 6905389 Invader/BgIII 0.42
LRP5 g.23715C→A ○ 6905390 NT
LRP5 g.24964C→T ♦ 6905391 Invader/RFLP(MnII) 0.14
LRP5 g.26659A→G ♦ 6905392 NT
LRP5 g.27081G→C ♦ 6905393 NT
LRP5 g.28047T→C ♦ 6905394 NT
LRP5 g.28149C→T ♦ 6905395 Invader/RFLP(MboII) 0.42
LRP5 g.29652T→C ♦ 6905396 NT
LRP5 g.29925T→C ♦ 6905397 NT
LRP5 g.31502G→A ○ 6905398 NT
LRP5 g.31856G→A ○ 6905399 Invader/RFLP(DpnI) 0.094
LRP5 g.34749G→A ■ 6905400 NT
LRP5 g.35592T→C ♦ 6905401 Invader 0.44
LRP5 g.37442A→C ♦ 6905402 NT
LRP5 g.37679G→A ♦ 6905403 NT
LRP5 g.38270G→A ♦ 6905404 NT
LRP5 g.38393C→T ♦ 6905405 NT
LRP5 g.38590C→T ♦ 6905406 NT
LRP5 g.38885C→A ♦ 6905407 NT
LRP5 g.39440A→G ♦ 6905408 NT
LRP5 g.39807T→G ♦ 6905409 NT
LRP5 g.40495C→G ♦ 6905410 NT
LRP5 g.42125G→T ♦ 6905411 Invader 0.44
LRP5 g.43231G→A ○ 6905412 NT
LRP5 g.43404A→G ♦ 6905413 NT
LRP5 g.43718G→A ♦ 6905414 NT
LRP5 g.44602insC ♦ 6905415 NT
LRP5 g.45704G→A ♦ 6905416 Invader 0.44
LRP5 g.47698G→A ♦ 6905417 NT
LRP5 g.75326G→A ■ 6905418 RFLP/HphI 0.19
LRP5 g.78477G→A ■ 6905419 NT
LRP5 g.92423G→A graphic 6905438 RFLP/Tsp451 0.017
LRP5 g.95318G→A ■ 6905420 NT
LRP5 g.95385G→A ■ 6905421 RFLP/HaeIII 0.05
LRP5.30g.5276C→TASN740 ■ 6905422 ARMS 0.16
LRP5 30g.5380C→T ■ 6905425 ARMS 0.07
LRP5 30g.6891C→T ■ 6905426 ARMS 0.07
LRP5 30g.19977T→G ■ 6905423 NT
LRP5 30g.20149A→G ■ 6905424 NT
LRP5 30g.24930C→T graphic 6905439 cRFLP/NdeI 0.31
LRP5 30g.29264C→T ■ 6905351 RFLP/AciI 0.16
LRP5 30g.34160G→C graphic 6905440 RFLP/RsaI 0.08
LRP5 30g.34295T→C graphic 6905441 cRFLP/MspA11 0.006
C11orf23 c.3297-3302del ○ 6905347 Invader/length polymorphism 0.25
C11orf23 c.3488G→A ○ 6905348 Invader/cRFLP(NlaIII) 0.32
C11orf23 c.3680G→A ○ 6905349 Invader/ 0.24

  • ↵○ = Identified initially from cosmid/BAC overlaps.

  • ♦ = Identified initially from shotgun sequencing of 5-kb-long PCR products.

  • ■ = Identified initially by directed PCR amplification and sequencing of the LRP5 gene.

  • Graphic = Identified from dHPLC.

  • ↵NT = not tested.

This Article

  1. Genome Res. 13: 845-855

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