Table 1 Significant rare ( < 0.1%) non-coding genomic aggregate associations with human height after adjusting for known height loci (‘log10p conditioned’)

From: Whole-genome sequencing in 333,100 individuals reveals rare non-coding single variant and aggregate associations with height

CHR

START (b38)

END (b38)

CLASS

GENE/UNIT

Annotation

TEST

BETA (SD)

SE (SD)

p

p conditioned

p conditioned + 

Replication P-Value

6

34233791

34238791

Proximal

HMGA1

Upstream & Upstream (JARVIS > 0.99)

ACAT

NA

NA

1.58E-11

1.55E-10

3.72E-07

0.00183a

17

7017304

7023304

Proximal

C17orf49

Downstream (GERP > 2)

BURDEN

0.14

0.02

1.26E-11

1.26E-11

2.00E-11

1.40E-02

17

63918839

63923839

Proximal

GH1

Upstream (GERP > 2)

BURDEN

−0.33

0.05

5.01E-12

2.00E-12

4.27E-04

2.86E-01

22

44809805

44814805

Proximal

PRR5-ARHGAP8

Upstream (JARVIS > 0.99)

SKAT

NA

NA

3.72E-10

4.37E-10

4.72E-10

NA

  1. The CLASS column denotes how variants were classified according to Fig. 1, and the annotation column denotes how the variants were additionally grouped together (see “methods”) based on variant scores. Replication was calculated as a meta-analysis of TOPMed, All of Us and non-EUR analyses within UKB. a Indicates that the meta-analysis was calculated using the ACAT p-value combination method, as betas are not produced for the ACAT aggregate tests.
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