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Background  Our preliminary work confirmed that,  SLC22A7  (solute carrier family 22 member 7),  NGFR  (nerve growth factor receptor),  ARNTL  (aryl hydrocarbon receptor nuclear translocator like) and  PPP2R2B  (protein phosphatase 2 regulatory subunit Bβ) genes were differentially expressed in dairy cows during different stages of lactation, and involved in the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, so we considered these four genes as the candidates affecting milk production traits. In this study, we detected polymorphisms of the four genes and verified their genetic effects on milk yield and composition traits in a Chinese Holstein cow population.    Results  By resequencing the whole coding region and part of the flanking region of  SLC22A7 ,  NGFR ,  ARNTL  and  PPP2R2B , we totally found 20 SNPs, of which five were located in  SLC22A7 , eight in  NGFR , three in  ARNTL , and four in  PPP2R2B . Using Haploview4.2, we found three haplotype blocks including five SNPs in  SLC22A7 , eight in  NGFR  and three in  ARNTL . Single-SNP association analysis showed that 19 out of 20 SNPs were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage in the first and second lactations ( P  < 0.05). Haplotype-based association analysis showed that the three haplotypes were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage ( P  < 0.05). Further, we used SOPMA software to predict a SNP, 19:g.37095131C > T in  NGFR , changed the structure of NGFR protein. In addition, we used Jaspar software to found that four SNPs, 19:g.37113872C > G,19:g.37113157C > T, and 19:g.37112276C > T in  NGFR  and 15:g.39320936A > G in  ARNTL , could change the transcription factor binding sites and might affect the expression of the corresponding genes. These five SNPs might be the potential functional mutations for milk production traits in dairy cattle.    Conclusions  In summary, we proved that  SLC22A7 ,  NGFR ,  ARNTL  and  PPP2R2B  have significant genetic effects on milk production traits. The valuable SNPs can be used as candidate genetic markers for genomic selection of dairy cattle, and the effects of these SNPs on other traits need to be further verified.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12863-021-01002-0.

Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein