Table 2. Novel loci identified in the discovery stage.
| SNP | chr:pos | Gene | CA/NCA | CAF (%) (AA/HA/EA) |
Minority meta-analysis |
AA-specific meta-analysis | HA-specific meta-analysis | Minority + European | Combined replication 1 |
Discovery + Replication | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BETA | P | BETA | P | BETA | P | BETA | P | Z | P | Z | P | |||||
| HDL | ||||||||||||||||
| rs17102282 | 5:144103408 | 5q31 | A/G | 47/25/12 | 0.040 | 3.3E-8 | 0.044 | 4.9E-5 | 0.045 | 3.2E-5 | 0.023 | 1.1E-5 | 2.3 | 0.022 | 3.8 | 1.7E-4 |
| rs11782435 | 8:13536115 | DLC1 | T/C | 8.9/13/22 | 0.063 | 6.8E-10 | 0.014 | 0.47 | 0.085 | 8.8E-10 | 0.023 | 8.6E-6 | 2.6 | 9.6E-3 | 4.1 | 4.6E-5 |
| rs145312881 | 9:89053469 | ZCCHC6 | A/G | 0.37/0/0 | 0.50 | 1.6E-8 | 0.46 | 1.1E-6 | - | - | - | - | 0.93 | 0.35 | 3.7 | 1.8E-4 |
| rs75405126 2 | 14:53797383 | DDHD1 | T/C | 0/0/0.10 | 0.76 | 2.1E-8 | - | - | - | - | 0.49 | 8.8E-5 | -0.16 | 0.88 | 3.2 | 1.2E-3 |
| rs12940636 | 17:53400110 | HLF | C/T | 20/24/34 | 0.025 | 1.3E-3 | 0.035 | 9.2E-3 | 0.025 | 0.025 | 0.025 | 9.1E-9 | 4.5 | 6.6E-6 | 6.3 | 2.3E-10 |
| LDL | ||||||||||||||||
| rs35882350 | 12:623129 | B4GALNT3 | G/A | 19/16/25 | 0.033 | 1.2E-3 | 0.040 | 9.9E-3 | 0.026 | 0.054 | 0.033 | 1.2E-10 | 6.3 | 4.1E-10 | 8.2 | 3.0E-16 |
| rs3747910 | 20:5528518 | GPCPD1 | G/A | 25/17/21 | -0.028 | 2.4E-3 | -0.033 | 9.4E-3 | -0.026 | 0.038 | -0.028 | 2.1E-8 | -5.6 | 2.5E-8 | -7.2 | 5.3E-13 |
| TC | ||||||||||||||||
| rs903381 | 5:95399878 | PCSK1 | A/G | 3.8/0.85/0 | 0.10 | 2.6E-4 | 0.039 | 0.17 | 0.34 | 2.8E-8 | - | - | -0.78 | 0.43 | 0.44 | 0.66 |
| rs35882350 | 12:623129 | B4GALNT3 | G/A | 19/16/25 | 0.028 | 3.8E-3 | 0.027 | 0.078 | 0.025 | 0.056 | 0.028 | 2.0E-8 | 5.8 | 8.0E-9 | 7.4 | 9.8E-14 |
| rs199986018 | 20:5544985 | GPCPD1 | C/A | 24/17/21 | -0.038 | 2.0E-4 | -0.036 | 4.6E-3 | -0.037 | 2.8E-3 | -0.038 | 1.4E-8 | -4.9 | 9.6E-7 | -6.4 | 1.5E-10 |
| TG | ||||||||||||||||
| rs182013227 | 2:74612959 | MTHFD2 | C/T | 0.39/0/0 | 0.54 | 5.7E-10 | 0.57 | 3.6E-9 | - | - | - | - | 0.73 | 0.46 | 2.7 | 6.1E-3 |
SNP, single nucleotide polymorphism; chr, chromosome; pos, position; CA, coding allele; NCA, non-coding allele; CAF, coding allele frequency; AA, African American; HA, Hispanic-ancestry; EA, European-ancestry.
1 The combined replication results were generated through meta-analyzing all replication datasets. Ancestry-specific replication results are shown in S5 Table.
2 This variant was mainly driven by signal in Hawaiians (MAF = 0.79%, BETA = 0.95, PHawaiian = 2.7E-7) and details are presented in S3 Table.