Dataset of allele, genotype and haplotype frequencies of four LIN28B gene polymorphisms analyzed for association with age at menarche in Russian women.

The dataset represents the raw data (supplementary Table), frequencies of alleles, genotypes and haplotypes for single nucleotide polymorphisms (SNPs) rs4946651, rs7759938, rs314280 and rs314276 of the LIN28B gene associated with age at menarche in previously published genome-wide and candidate gene association studies https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738205/ , [1] , [2] , [3] , [4] , [5] , [6] , [7] . The data were divided into three groups according to the age at menarche (AAM) of the participants: the whole sample, the early age at menarche (<12 years), and the average age at menarche (12–14 years). The frequencies of the alleles, genotypes and haplotypes are presented in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738205/table/t0005/ , Table 1 and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738205/table/t0010/ , Table 2 respectively. The structure of linkage disequilibrium of rs4946651, rs7759938, rs314280 and rs314276 in LIN28B gene is shown in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738205/figure/f0005/ , Fig. 1 . Table 1 The frequencies of alleles and genotypes for single nucleotide polymorphisms (SNPs) rs4946651, rs7759938, rs314280 and rs314276 of the LIN28B gene in the sample of Russian women. Table 1 SNP genotype or allele All (n = 674) Age at menarche Mean, years early (<12 yrs) (n = 66) average (12–14 yrs) (n = 579) n frequency n frequency n frequency rs4946651 AA 120 0.1780 12.67 ± 1.00 8 0.1212 108 0.1865 GA 333 0.4941 12.65 ± 1.09 35 0.5303 282 0.4870 GG 221 0.3279 12.56 ± 1.03 23 0.3485 189 0.3265 A 573 0.4251 – 51 0.3864 498 0.4301 G 775 0.5749 – 81 0.6136 660 0.5699 rs7759938 CC 52 0.0772 12.73 ± 1.12 4 0.0606 45 0.0777 TC 298 0.4421 12.67 ± 1.07 28 0.4242 255 0.4404 TT 324 0.4807 12.56 ± 1.03 34 0.5152 279 0.4819 C 402 0.2982 – 36 0.2727 345 0.2979 T 946 0.7018 – 96 0.7273 813 0.7021 rs314280 TT 109 0.1617 12.68 ± 1.01 8 0.1212 97 0.1675 CT 344 0.5104 12.65 ± 1.09 35 0.5303 293 0.5060 CC 221 0.3279 12.56 ± 1.03 23 0.3485 189 0.3265 T 562 0.4169 – 51 0.3864 487 0.4206 C 786 0.5831 – 81 0.6136 671 0.5794 rs314276 AA 63 0.0935 12.68 ± 1.10 6 0.0909 54 0.0933 CA 300 0.4451 12.71 ± 1.07 25 0.3788 259 0.4473 CC 311 0.4614 12.53 ± 1.02 35 0.5303 266 0.4594 A 426 0.3160 – 37 0.2803 367 0.3169 C 922 0.6840 – 95 0.7197 791 0.6831 Table 2 The frequencies of haplotypes for single nucleotide polymorphisms (SNPs) rs4946651, rs7759938, rs314280 and rs314276 of the LIN28B gene in the sample of Russian women. Table 2 Haplotype (rs4946651, rs7759938, rs314280 and rs314276 All (n = 674), frequency Age at menarche early (<12 yrs) (n = 66), frequency average (12–14 yrs) (n = 579), frequency ACTA 0.287 0.265 0.287 GTCA 0.024 0.015 0.024 ATTC 0.122 0.114 0.126 GTCC 0.551 0.598 0.547 Fig. 1 The structure of linkage disequilibrium of rs4946651, rs7759938, rs314280 and rs314276 in the LIN28B gene in the sample of Russian women. Linkage disequilibrium was measured by Lewontin's coefficient D′. The dark red (D′ = 1) indicates that there exists strong pairwise LD between SNPs. A) All sample set. B) Early age at menarche (<12 years). C) Average age at menarche (12–14 years). Fig. 1 The frequencies of alleles and genotypes for single nucleotide polymorphisms (SNPs) rs4946651, rs7759938, rs314280 and rs314276 of the LIN28B gene in the sample of Russian women. The frequencies of haplotypes for single nucleotide polymorphisms (SNPs) rs4946651, rs7759938, rs314280 and rs314276 of the LIN28B gene in the sample of Russian women. The structure of linkage disequilibrium of rs4946651, rs7759938, rs314280 and rs314276 in the LIN28B gene in the sample of Russian women. Linkage disequilibrium was measured by Lewontin's coefficient D′. The dark red (D′ = 1) indicates that there exists strong pairwise LD between SNPs. A) All sample set. B) Early age at menarche (<12 years). C) Average age at menarche (12–14 years).

The recruitment of the participants was carried out through the Perinatal Centre of the Belgorod Regional Clinical Hospital of St. Joasaph during 2008–2013. All participants were unrelated women of Russian descent (self-declared) living in Central Russia [8] . The following exclusion criteria were adopted: non-Russian descent, a birthplace outside of Central Russia, malignant tumors of a small pelvis and breast, benign tumors and hyperplastic disorders of the reproductive organs in women (leiomyoma, endometriosis, and endometrial hyperplasia), chronic severe diseases of the vital organs (heart, respiratory or renal failure), severe autoimmune diseases. The research protocol was approved by the Regional Ethics Committee of Belgorod State University. Written informed consent for participation was obtained from all individuals enrolled in the research. The information about AAM was obtained using the questionnaire. AAM was defined as age (full years) of first menses. Each participant was asked a question: “How old were you when you had the first menses?” Women with AAM ≥18 years (n = 4) or women who refused to answer (n = 13) were excluded from the research. In total, 674 females participated in the research. The phlebotomy was performed by a certified nurse. Five milliliters of blood was taken from the ulnar vein into a plastic vial (Vacutainer®) with 0.5M EDTA solution (рН = 8.0). Extraction of lymphocyte DNA was done by standard phenol-chloroform technique and quantified by Nanodrop 2000 spectrophotometer (Thermo Scientific, Inc.). Only samples with А260/А280 = 1.7–2.0 were used for the analysis. The 4 SNPs in the LIN28B gene (rs4946651, rs7759938, rs314280 and rs314276) were selected for the analysis based on the following criteria [9] , [10] : 1) Previously reported associations with AAM and phenotypes, which share metabolic pathways with menarche (e.g., obesity, anthropometric characteristics, vitamin D metabolism, etc.), 2) Regulatory potential (regSNP), 3) Effect on gene expression (eSNP), 4) Tag value (tagSNP) and 5) MAF > 5%. The selected polymorphic loci have functional significance: all SNPs appear to have a significant regulatory potential ( Table 3 ) (determined using the online tools HaploReg, v4.1 update 05.11.2015, https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php ) and to influence gene expression level ( Table 4 ) (determined using the GTExportal data, http://www.gtexportal.org/ ). Table 3 Regulatory effects of the 4 SNPs of the LIN28B gene (HaploReg, v4.1, update 05.11.2015) ( https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php ). Table 3 pos (hg38) variant Ref Alt AFR AMR ASN EUR GERP SiPhy Promoter Enhancer DNAse Proteins Motifs NHGRI/EBI GRASP QTL Selected eQTL GENCODE dbSNP freq freq freq freq cons cons histone marks histone marks bound changed GWAS hits hits hits genes func annot 104921635 rs4946651 A G 0.18 0.63 0.70 0.52 1 hit 15kb 3′ of LINC00577 104931079 rs7759938 C T 0.37 0.72 0.70 0.65 ESC, IPSC 6 hits 2 hits 5.2kb 3′ of LINC00577 104952962 rs314280 A G 0.18 0.62 0.70 0.52 6 tissues 4 tissues 11 tissues 5 bound proteins 1 hit 1 hit 4.1kb 5′ of LIN28B 104960124 rs314276 A C 0.53 0.67 0.70 0.64 5 tissues IPSC HNF1,OTX,Pou2f2 2 hits 11 hits LIN28B intronic Table 4 The cis-eQTL values of the 4 SNPs of the LIN2B gene (according to Genotype-Tissue Expression (GTEx) ( http://www.gtexportal.org/ )). Table 4 SNP Gene expression Allele ref Allele alt Effect Size (β) P-Value Tissue rs4946651 LIN28B A G −0.40 7.6х10 -8 Pituitary LINC00577 0.58 0.0000016 Brain - Cortex LINC00577 0.48 0.0000022 Brain - Putamen (basal ganglia) rs7759938 LIN28B C T −0.50 1.3х10 -11 Pituitary rs314280 LIN28B A G −0.40 7.6х10 -8 Pituitary LINC00577 0.58 0.0000016 Brain - Cortex LINC00577 0.48 0.0000022 Brain - Putamen (basal ganglia) rs314276 LIN28B A C −0.50 9.4х10 -12 Pituitary Regulatory effects of the 4 SNPs of the LIN28B gene (HaploReg, v4.1, update 05.11.2015) ( https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php ). The cis-eQTL values of the 4 SNPs of the LIN2B gene (according to Genotype-Tissue Expression (GTEx) ( http://www.gtexportal.org/ )). DNA samples were genotyped using the Sequenom MassARRAY® iPLEX platform at the Centre of Genomic Sciences (University of Hong Kong). The procedure for DNA sample preparation and data quality control are described elsewhere [10] . The correspondence of the SNPs to the Hardy-Weinberg equilibrium was checked using the chi-square test. No significant differences in allele frequencies between the group with the early age at menarche ( 0.05) were revealed. The Haploview version 4.2 software ( https://www.broadinstitute.org/haploview/haploview ) was used to quantify the linkage disequilibrium (LD) between rs4946651, rs7759938, rs314280 and rs314276 in LIN28B gene. Haplotype frequencies were determined using the EM algorithm. The LD block structure was defined using the Solid Spine of the LD algorithm [11] provided by the Haploview 4.2. The degree of genetic linkage between the 4 SNPs in each groups was estimated as Lewontin's coefficient D′, where no color (D′ = 0) indicates that LD is weak or nonexistent and the dark red (D′ = 1) indicates that there exists strong pairwise LD between SNPs ( Fig. 1 ).