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Fig. 2 | BMC Cancer

Fig. 2

From: A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci

Fig. 2

eQTL analysis of the rs9911630- BRCA1 variant in different populations. a rs9911630 was tested for correlation with BRCA1 gene expression using the eQTL database GENe Expression VARiation (Genevar) from Sanger institute plateform. eQTLs in 8 different HapMap populations are showed in this figure (CEU: Utah residents with Northern and Western European ancestry from the CEPH, CHB: Han Chinese in Beijing, China; JPT: Japanese in Tokyo, Japan; GIH: Gujarati Indians in Houston, MEX: Mexican ancestry in Los Angeles, California; YRI: Yoruba in Ibadan, Nigeria; LWK: Luhya in Webuye, Kenya; MKK: Maasai in Kinyawa, Kenya). The 8 Box plots represent BRCA1 expression levels on the y axis with respect to the rs9911630 genotypes showed on the x axis. P values (P) < 0.05 means significant eQTL associations. b eQTL association results across different HapMap populations are shown on the y axis (log10). The chromosomal position of the BRCA1 gene (chr17:38449840–38,530,994 according to NCBI36/hg18 assembly) is shown on the x axis. eQTL peaks represent the significant eQTL correlation that have been observed for rs9911630 in Caucasian, Chinese and Japanese samples. c Haplotype blocks constructed with variants identified in the Tunisian subjects showing a frequency ≥ 5%. Tagging SNPs identified on a block-by-block basis are denoted with an arrow below the SNP number. Tunisian haplotype frequencies are displayed on the right of each haplotype combination, while the level of recombination is displayed below the connections between the blocks. Thick connections represent haplotypes with frequencies ≥5%, while frequencies below 5% are represented by thin lines. Variant #12 is rs9911630

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