In relation to the above comments I just wanted to add a small example of a manhatten plot with addition of rs number (or genes) in R:

generation of a data set

pval<-runif(100000, 0, 1); logPval<--log(pval,base=10); pos=1:100000; chr<-paste("chr",rep(1:20,ea=5000),sep=""); rsID<-paste("rs",1:100000,sep=""); data<-as.data.frame(cbind(chr,pos,rsID,pval,logPval));

vectors that defines color

vek<-as.numeric(gsub(data$chr,pattern="chr",replacement=""))%%2

vector that defines which dot should have a rs number (all with pval<0.0001)

vek2<-ifelse(as.numeric(as.character(data[,"pval"]))<0.0001,T,F)

plotting

plot(x=as.numeric(data$pos),y=as.numeric(as.character(data$logPval)),col=c("red","blue")[as.factor(vek)])

adding the text

text(labels=as.character(data$rsID[vek2]),x=as.numeric(data$pos)[vek2],y=as.numeric(as.character(data$logPval))[vek2],pos=4,cex=0.8)

If I look at this plot I would almost think that these are placed there by hand.

I'm not sure how your Manhattan plot looks like right now (did you use any package?) but Getting Genetics Done has quite some nice code examples about making a Manhattan plot and QQ plot in R using ggplot2

If you are willing to leave R you could also look at WGA viewer which can plot your Manhattan plot and add different data tracks next to it.

If you're just interested in showing the association later for a specific region I would recommend using LocusZoom, that tool can plot gene names + locations and adds LD information to a locus of interest.