Table 1 MPRA variants tested in transgenic mouse assay

From: Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity

Variant name

Reference MPRA activity

Variant MPRA effect

TFBS affected

VISTA element

Structures affected in transgenic assay

Neural target genes

Relevant target gene phenotypic associations

chr6−162856979-C-G

2

−1.9

RORB (gain), CTCF

hs2793.1

partial forebrain loss

QKI, PACRG and PRKN

Associated with Parkinson’s Disease (PACRG, PRKN) and schizophrenia (QKI)

chr6-97306759-A-T

1.9

−2.2

CDX1 (gain), POU4F1

hs978.1

partial forebrain, hindbrain and neural tube loss

GPR63

Branchiooculofacial Syndrome and Spina Bifida Occulta

chr1-52663061-C-G

3.1

−2.4

SP2

hs2790.1*

midbrain gain, partial forebrain loss

COA7, TUT4 and others

Spinocerebellar Ataxia (COA7) Perlman Syndrome (TUT4)

chr13-80276542-C-G

0.2

+6.7

NFY (gain)

hs3117.1*

midbrain and hindbrain gain

SPRY2

Decreased brain expression in schizophrenia and bipolar disorder

chr5-88396638-C-G

−0.1

−1.3

ASCL1 (gain), NR2F1

hs268.1

no effect

MEF2C

Associated with cognitive disability, epilepsy and cerebral malformations

  1. TFBS predictions from motifbreakR. Motifs consistent with variant effects in bold (see Fig. 4c). Neural target genes found using activity-by-contact (ABC) on data from WTC11 excitatory neurons (cell line used in this study) or prenatal week 18 prefrontal cortex neurons (Methods).
  2. *Element not previously tested in the transgenic assay.
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