You can use the select method to extract particular columns and rows. According to your dataset, you can use the below-given code.
IND snp1 snp2 snp3 snp4 snp5
1 1 A/G T/T T/C G/C G/G
2 2 A/A C/C G/G G/G A/A
3 3 T/T G/G C/C C/C T/T
> select(df, snp1,snp3,snp4)[1,1:3]
snp1 snp3 snp4
1 A/G T/C G/C
I hope this will give you the approach.