Table 1 Datasets

Differential analysis: alleles

Tewhey

Study of 39,479 oligos coming from 29,173 variants

NA12878 (LCL)

NA12878: 5

79k pool: ∼73

to follow up on prior eQTL results.

NA19239 (LCL)

NA19239: 3

7.5k pool: ∼350

Large initial oligo pool: 79k. Second pool: 7.5k.

HepG2

HepG2: 5

Ulirsch

Study of 2756 variants in strong LD with 75 main

K562, K562 with

K562: 6

14

variants to identify loci that affect RBC traits.

GATA1 over-expr.

K562+GATA1: 4

Differential analysis: conditions

Inoue

Comparison of episomal and lentiviral MPRA.

HepG2

3

Max: 99

Shen

Study of tissue specificity of cis-regulatory

Mouse retina and

3

∼8

element in-vivo in mouse.

cerebral cortex

Saturation mutagenesis

Melnikov

Two inducible enhancers:

HEK293T

Single: 2

Single: 13

(1) a synthetic cAMP-regulated enhancer and

Multi: 2

Multi: 1

(2) the virus-inducible interferon-beta enhancer.

Single-hit scanning alters one base at a time.

Multi-hit sampling alters several bases at a time.

Kheradpour

Study of 2104 wild-type sequences and 3314 variant

K562

2

10

sequences containing targeted motif disruptions to

HepG2

understand base-level effects in motifs.