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作者：小丫  来源： 嘉因

小丫经常介绍一些好用的工具，例如整合了eQTL、DNase-seq、ChIP-seq数据和motif分析的检索工具HaploReg和Regulome，用它们查询SNP对转录调控的影响、挖掘变异导致表型变化的机制，非常方便、好用、直观，详见《non-coding区的SNP影响了转录？HaploReg视频》和《变异会影响转录？SNP影响转录因子结合？RegulomeDB》

怎样把查询结果用到自己的课题里？

写paper时怎样展示结果？

小丫特意检索了哪些文章用到了HaploReg和Regulome，画出怎样的结果图。评选出卖家秀和买家秀。今天赏图，下期详细看文章。

Figure 4 T2D GWAS SNPs in a muscle-specific stretch enhancer of ANK1 provide mechanistic insights into T2D pathophysiology in skeletal muscle.

出自Scott, L. J., Erdos, M. R., Huyghe, J. R., Welch, R. P., Beck, A. T., Wolford, B. N., ... & Taylor, D. L. (2016). The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Naturecommunications, 7, 11764. （影响因子：12.124）

Table 2. Significant enrichment of 45 MI/CAD-associated SNPs in specific cell types detected by enrichment analysis

Fig. 2 Polygenic, enrichment and heritability analysis of three histone modification marks across cell types.

出自Won, H.H., Natarajan, P., Dobbyn, A., Jordan, D.M., Roussos, P., Lage, K., Raychaudhuri, S., Stahl, E. and Do, R., 2015. Disproportionate contributions of select genomic compartments and cell types to genetic risk for coronary artery disease. PLoS genetics, 11(10), p.e1005622.（影响因子：6.100）

买家秀

Supplementary Figure 5. Functional annotations of associated variants from Haploreg 4.1.

出自Lane, J. M., Liang, J., Vlasac, I., Anderson, S. G., Bechtold, D. A., Bowden, J., ... & Loudon, A. (2017). Genome-wide association analyses of sleep disturbance traits identify new loci and highlight shared genetics with neuropsychiatric and metabolic traits. Nature genetics, 49(2), 274. (影响因子：27.959)

Table S1 Comparisons of rare variant burden in subsets of SNPs and Genes

出自Zhao, J., Akinsanmi, I., Arafat, D., Cradick, T. J., Lee, C. M., Banskota, S., ... & Gibson, G. (2016). A burden of rare variants associated with extremes of gene expression in human peripheral blood. The American Journal of Human Genetics, 98(2), 299-309. （影响因子：9.025）

Table 1 Fifteen SNPs tagged by rs9828519 with r2 ≥0.8

出自Liu, G., Zhang, F., Hu, Y., Jiang, Y., Gong, Z., Liu, S., ... & Hao, J. (2017). Genetic variants and multiple sclerosis risk gene SLC9A9 expression in distinct human brain regions. Molecularneurobiology, 54(9), 6820-6826. (影响因子：6.19)

下面几篇的作者超爱这俩工具：

Guo, L., Peng, Y., Sun, L., Han, X., Xu, J., & Mao, D. (2017). Ovarian cancer variant rs2072590 is associated with HOXD1 and HOXD3 gene expression. Oncotarget, 8(61), 103410.

（影响因子：5.168）

Liu, L., Zuo, X., Zhu, Z., Wen, L., Yang, C., Zhu, C., ... & Zheng, X. (2018). Genome‐wide association study identifies three novel susceptibility loci for systemic lupus erythematosus in Han Chinese. British Journal of Dermatology.(影响因子：4.706)

Zhang, Y. M., Zhou, X. J., Nath, S. K., Sun, C., Zhao, M. H., & Zhang, H. (2017). Evaluation of 10 SLE susceptibility loci in Asian populations, which were initially identified in European populations. Scientific Reports, 7, 41399.

（影响因子：4.259）

Campo, C., Silva Filho, M. I., Weinhold, N., Mahmoudpour, S. H., Goldschmidt, H., Hemminki, K., ... & Försti, A. (2017). Bortezomib‐induced peripheral neuropathy: A genome‐wide association study on multiple myeloma patients. Hematological oncology.（影响因子：3.118）

Wang, H., Wang, Z., Rani, P. L., Fu, X. A., Yu, W., Bao, F., ... & Yue, Z. (2017). Identification of PTPN22, ST6GAL1 and JAZF1 as psoriasis risk genes demonstrates shared pathogenesis between psoriasis and diabetes. Experimental dermatology. （影响因子：2.679）

Campo, C., Da Silva Filho, M. I., Weinhold, N., Goldschmidt, H., Hemminki, K., Merz, M., & Försti, A. (2017). Genetic susceptibility to bortezomib-induced peripheral neuroropathy: replication of the reported candidate susceptibility loci. Neurochemical research, 42(3), 925-931.(影响因子：2.581)

唯有这篇，影响因子：无，这应该是真爱了：

Zhang, Y. M., Zhou, X. J., Cheng, F. J., Qi, Y. Y., Hou, P., Zhao, M. H., & Zhang, H. (2016). Polymorphism rs3828903 within MICB is associated with susceptibility to systemic lupus erythematosus in a Northern Han Chinese population. Journal of immunology research, 2016. (影响因子：无)

送给读到最后的小伙伴一个福利：

Using haploR, an R package for querying HaploReg and RegulomeDB

Ilya Y. Zhbannikov

Tue Oct 31 19:06:51 2017

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