Import the table from the CSV or txt file and create the following three tables.
test1 a,
     test42b,
     test53 c

and then join it.

Hope this one works.
PROC SQL;

create table test as

select

 a.SNP_id
,a.allele1_Forward as a1_1
,a.allele2_Forward as a2_1
,b.allele1_Forward as a1_42
,b.allele2_Forward as a2_42
,c.allele1_Forward as a1_53
,c.allele2_Forward as a2_53

from test1 a,
     test42b,
     test53 c

where a.snp_id=b.snp_id and b.snp_id=c.snp_id;
quit;

proc print data=test;
run;