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Table 2 Genes linked to SNPs identified in the GWA analysis for PVL and WBCs

From: Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

refSNP_ID

Position a

A1 b

MAF

Variant type c

Symbol d

Description

rs110155623

20,692,320

A

0.03

Regulatory intergenic

GPR111, CD2AP

G protein-coupled receptor 111; CD2-associated protein

rs41587216

22,300,959

A

0.46

Intergenic

CRISP1

Cysteine-rich secretory protein 1

rs41566363

22,997,898

C

0.33

Regulatory intergenic

TFAP2D

Transcription factor AP-2 delta (activating enhancer binding protein 2 delta)

rs41641297

24,181,053

A

0.40

Intronic

PKDH1

Polycystic kidney and hepatic disease 1

rs109343703

24,699,202

A

0.12

Intronic

TRAM2

Translocation associated membrane protein 2

rs110499907

24,727,613

A

0.14

Intergenic

TRAM2

Translocation associated membrane protein 2

rs110473048

25,109,188

A

0.34

Intergenic

GCM-1

Glial cells missing homolog 1

rs110525467

25,426,985

G

0.19

Synonymous substitution

BOLA-DQA1

Major histocompatibility complex, class II, DQA1

rs110579760

25,507,676

G

0.12

Intergenic

BOLA-DRB3

Major histocompatibility complex, class II, DRB3

rs110836188

27,088,825

G

0.21

Synonymous substitution

TNXB

Tenascin-X precursor

rs41255514

27,305,227

G

0.34

3′-UTR

SCL44A4

Solute carrier family 44, member 4

rs17872223

27,306,795

G

0.33

Intronic

NEU1

Sialidase 1 (lysosomal sialidase)

rs110861313

27,444,064

C

0.46

Regulatory intergenic

C23H6ORF47, ABHD16A, LY6G5C, LY6G5B, CSNK2B, BAT4, APOM, BAG6

Chromosome 23 open reading frame, human C6orf47; Abhydrolase domain containing 16A; Lymphocyte antigen 6 complex, locus G5C; Lymphocyte antigen 6 complex, locus G5B; Casein kinase 2, beta polypeptide; G patch domain and ankyrin repeats 1; Apolipoprotein M; BCL2-associated athanogene 6

rs17871874

27,485,467

A

0.24

Synonymous substitution

PRRC2A

Proline-rich coiled-coil 2A

rs110260956

27,545,231

G

0.15

Regulatory intergenic

LTA, NFKBIL1, ATP6V1G2,LTB,TNF

Lymphotoxin alpha; Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1; ATPase, H+ transporting, Lysosomal 13 kDa, V1 subunit G2; Lymphotoxin beta; Tumor necrosis factor

rs110350951

27,841,983

G

0.44

Regulatory intergenic

U6, Ig_like_MHC_I

U6 small nuclear RNA; Major histocompatibility complex, class I, A-like

rs110794231

27,887,914

A

0.38

Intergenic

BOLA

Bola class I

rs41587536

27,923,154

G

0.38

Intergenic

SFTA2

Surfactant associated 2

rs110742604

28,087,630

G

0.20

Regulatory intergenic

TUBB5, IER3, FLOT1

Tubulin, beta class I; Immediate early response 3; Flotillin 1

rs109856572

28,649,349

A

0.41

Regulatory intergenic

TRIM31, TRIM40

Tripartite motif containing 31; Tripartite motif containing 40

rs110769723

29,285,952

G

0.18

Regulatory intergenic

LOC516273, LOC618064, LOC785162

Olfactory receptor; Olfactory receptor; Olfactory receptor

rs109015676

29,535,762

G

0.12

Regulatory intergenic

LOC784787,LOC511103, LOC784858

Olfactory receptor; Olfactory receptor; Olfactory receptor

rs110034224

30,662,593

C

0.17

Regulatory intergenic

LOC522315

Olfactory receptor

rs110277740

31,286,064

G

0.17

Regulatory intergenic

ABT1

Activator of basal transcription 1

rs109754326

33,296,630

G

0.34

Regulatory intergenic

NRSN1

Neurensin 1

  1. Abbreviations: refSNP_ID: dbSNP SNPs Identification (http://www.ncbi.nlm.nih.gov/SNP/), MAF: Minor Allelic Frequency, NA: Not Applicable
  2. aSNP location according to bovine genome assembly UMD3.1
  3. bAllele with the lowest frequency in the 50KSNP chip according to the Illumina nomenclature TOP/BOT
  4. cIntergenic: SNP positioned between 20 and 55 kb to the nearest gene; Regulatory intergenic: SNP positioned 0-20Kb upstream or downstream of a gene; Synonymous substitution: exonic SNP producing a synonymous amino acid substitution in the gene; 3’-UTR: SNP positioned in the 3′ untranslated region of a gene; Intronic: SNP positioned in gene introns
  5. dGene symbol according to UniProtKB (http://www.uniprot.org/)
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BMC Genomics

ISSN: 1471-2164

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