SCREEN V4 fields annotate overlap of each allele’s GRCh38 REF footprint with the original Registry V4 cCRE intervals. The retained ENCODE_cCRE_Annotation column is a separate legacy label. See field definitions.

Data license: Apache License 2.0

Variant_ID

Unique key Chromosome:Position:Ref:Alt (GRCh38)

RSID

dbSNP Reference SNP ID (build 156)

Chromosome

Chromosome (1-22; autosomes only)

Position

Genomic base-pair position (GRCh38)

Reference_Allele

Reference allele (GRCh38)

Alternate_Allele

Alternate (non-reference) allele

Joint_AF

gnomAD v4.1 joint alternate-allele frequency (all ancestries combined)

African_AF

gnomAD v4.1 joint AF, African / African-American

Admixed_American_AF

gnomAD v4.1 joint AF, Admixed American

Ashkenazi_Jewish_AF

gnomAD v4.1 joint AF, Ashkenazi Jewish

East_Asian_AF

gnomAD v4.1 joint AF, East Asian

Finnish_AF

gnomAD v4.1 joint AF, Finnish

Middle_Eastern_AF

gnomAD v4.1 joint AF, Middle Eastern

Non_Finnish_European_AF

gnomAD v4.1 joint AF, Non-Finnish European (the MAF >= 5% inclusion cohort)

South_Asian_AF

gnomAD v4.1 joint AF, South Asian

ENCODE_cCRE_Annotation

Legacy functional/regulatory label from the original annotation pipeline; not a SCREEN V4 cCRE class

SCREEN_V4_Classes

Distinct SCREEN Registry V4 GRCh38 cCRE classes overlapping the reference-allele interval; pipe-separated; empty string means no overlap

SCREEN_V4_Accessions

Distinct overlapping SCREEN Registry V4 EH38E element identifiers; pipe-separated; empty string means no overlap

SCREEN_V4_Overlap_Count

Number of distinct SCREEN V4 elements overlapping [Position-1, Position-1+length(REF)); zero means no overlap

Repeat_Name

RepeatMasker repeat name

Repeat_Class

RepeatMasker repeat class (LINE/SINE/LTR/DNA...)

Repeat_Family

RepeatMasker repeat family

Functional_Annotation

ANNOVAR/Ensembl region class (intergenic, intronic, exonic...)

Gene

Ensembl gene symbol(s) at/near the variant

Gene_Detail

Transcript / distance detail (ANNOVAR)

Exonic_Function

Coding consequence (nonsynonymous/synonymous/stopgain...)

Amino_Acid_Change

Amino-acid change & transcript (coding variants only)

PhastCons_100way

phastCons conservation, 100-way vertebrate (0-1)

PhyloP_100way

phyloP conservation, 100-way vertebrate (signed)

Evo2_7B_NoRC_Ref

Evo2-7B log-likelihood, REF sequence (no reverse-complement)

Evo2_7B_NoRC_Alt

Evo2-7B log-likelihood, ALT sequence (no reverse-complement)

Evo2_7B_NoRC_Delta

Evo2-7B delta = log P(ALT) - log P(REF). Strength is |delta|; the sign is the direction of the likelihood shift, not of a phenotypic effect

Evo2_7B_AvgRC_Ref

Evo2-7B log-likelihood, REF (avg of forward + reverse-complement)

Evo2_7B_AvgRC_Alt

Evo2-7B log-likelihood, ALT (avg of forward + reverse-complement)

Evo2_7B_AvgRC_Delta

Evo2-7B delta (ALT - REF), avgRC strategy

Evo2_7B_WeightedRC_Ref

Evo2-7B log-likelihood, REF (position-weighted RC)

Evo2_7B_WeightedRC_Alt

Evo2-7B log-likelihood, ALT (position-weighted RC)

Evo2_7B_WeightedRC_Delta

Evo2-7B delta (ALT - REF), wtRC strategy

Evo2_40B_NoRC_Ref

Evo2-40B log-likelihood, REF sequence (no reverse-complement)

Evo2_40B_NoRC_Alt

Evo2-40B log-likelihood, ALT sequence (no reverse-complement)

Evo2_40B_NoRC_Delta

Evo2-40B delta = log P(ALT) - log P(REF). Strength is |delta|; the sign is the direction of the likelihood shift, not of a phenotypic effect

Evo2_40B_AvgRC_Ref

Evo2-40B log-likelihood, REF (avg of forward + reverse-complement)

Evo2_40B_AvgRC_Alt

Evo2-40B log-likelihood, ALT (avg of forward + reverse-complement)

Evo2_40B_AvgRC_Delta

Evo2-40B delta (ALT - REF), avgRC strategy

Evo2_40B_WeightedRC_Ref

Evo2-40B log-likelihood, REF (position-weighted RC)

Evo2_40B_WeightedRC_Alt

Evo2-40B log-likelihood, ALT (position-weighted RC)

Evo2_40B_WeightedRC_Delta

Evo2-40B delta (ALT - REF), wtRC strategy

6,475,578 rows sorted by Evo2_40B_AvgRC_Delta descending

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CREATE TABLE variants (
  "Variant_ID" TEXT,
  "RSID" TEXT,
  "Chromosome" TEXT,
  "Position" INTEGER,
  "Reference_Allele" TEXT,
  "Alternate_Allele" TEXT,
  "Joint_AF" REAL,
  "African_AF" REAL,
  "Admixed_American_AF" REAL,
  "Ashkenazi_Jewish_AF" REAL,
  "East_Asian_AF" REAL,
  "Finnish_AF" REAL,
  "Middle_Eastern_AF" REAL,
  "Non_Finnish_European_AF" REAL,
  "South_Asian_AF" REAL,
  "ENCODE_cCRE_Annotation" TEXT,
  "Repeat_Name" TEXT,
  "Repeat_Class" TEXT,
  "Repeat_Family" TEXT,
  "Functional_Annotation" TEXT,
  "Gene" TEXT,
  "Gene_Detail" TEXT,
  "Exonic_Function" TEXT,
  "Amino_Acid_Change" TEXT,
  "PhastCons_100way" REAL,
  "PhyloP_100way" REAL,
  "Evo2_7B_NoRC_Ref" REAL,
  "Evo2_7B_NoRC_Alt" REAL,
  "Evo2_7B_NoRC_Delta" REAL,
  "Evo2_7B_AvgRC_Ref" REAL,
  "Evo2_7B_AvgRC_Alt" REAL,
  "Evo2_7B_AvgRC_Delta" REAL,
  "Evo2_7B_WeightedRC_Ref" REAL,
  "Evo2_7B_WeightedRC_Alt" REAL,
  "Evo2_7B_WeightedRC_Delta" REAL,
  "Evo2_40B_NoRC_Ref" REAL,
  "Evo2_40B_NoRC_Alt" REAL,
  "Evo2_40B_NoRC_Delta" REAL,
  "Evo2_40B_AvgRC_Ref" REAL,
  "Evo2_40B_AvgRC_Alt" REAL,
  "Evo2_40B_AvgRC_Delta" REAL,
  "Evo2_40B_WeightedRC_Ref" REAL,
  "Evo2_40B_WeightedRC_Alt" REAL,
  "Evo2_40B_WeightedRC_Delta" REAL
, MAF_tier TEXT, AF_bin TEXT, "SCREEN_V4_Classes" TEXT NOT NULL DEFAULT '', "SCREEN_V4_Accessions" TEXT NOT NULL DEFAULT '', "SCREEN_V4_Overlap_Count" INTEGER NOT NULL DEFAULT 0);
CREATE INDEX idx_chr_pos ON variants("Chromosome","Position");
CREATE INDEX idx_rsid ON variants("RSID");
CREATE INDEX idx_gene ON variants("Gene");
CREATE INDEX idx_variant ON variants("Variant_ID");
CREATE INDEX idx_7b_delta ON variants("Evo2_7B_NoRC_Delta");
CREATE INDEX idx_40b_delta ON variants("Evo2_40B_NoRC_Delta");
CREATE INDEX idx_func ON variants("Functional_Annotation");
CREATE INDEX idx_exonic ON variants("Exonic_Function");
CREATE INDEX idx_ccre ON variants("ENCODE_cCRE_Annotation");
CREATE INDEX idx_repclass ON variants("Repeat_Class");
CREATE INDEX idx_nfe_af ON variants("Non_Finnish_European_AF");
CREATE INDEX idx_joint_af ON variants("Joint_AF");
CREATE INDEX idx_maf_tier ON variants(MAF_tier);
CREATE INDEX idx_af_bin ON variants(AF_bin);
CREATE INDEX idx_40b_avgrc_delta ON variants(Evo2_40B_AvgRC_Delta);