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Table 1 Selected examples of human-specific regulatory elements tested in functional assays that showed gain or loss of function

From: Human evolution: the non-coding revolution

HAR Genome Location (hg19) Closest gene Experimental approach Biological function Domain of expression Reported functional difference Postulated phenotypic association Reference
HAR1 chr20:61,733,447–61,733,630 HAR1F; HAR1R qPCR; in situ hybridization RNA gene Cajal-Retzius neurons RNA secondary structure Brain development [18]
HAR2/HACNS1 chr2:236773664–236774209 AGAP1 (CENTG2); GBX2 Transgenic mice Enhancer Limb, branchial arches Gain of function Limb development [59]
2xHAR.142 chr14:34048651–34048815 NPAS3 Transgenic mice Enhancer Forebrain, midbrain, spinal cord Gain of function Brain development [57]
HAR202 chr14:34045570–34045772 NPAS3 Transgenic zebrafish Enhancer Central nervous system Loss of function Brain development [58]
ANC516 chr10:36238421–36239039 FZD8 Transgenic mice Enhancer Forebrain, midbrain, spinal cord Gain of function Brain development [56]
2xHAR.238 chr2:121832784–121833140 GLI2, TFCP2L1 Transgenic mice Enhancer Forebrain, midbrain, hindbrain and spinal cord Loss of function Brain development [37]
2xHAR.114 chr20:30425200–30425393 MYLK2, FOXS1 Transgenic mice Enhancer Limb and spinal cord Loss of function Limb development [37]
2xHAR.164 chr2:133346894–133347089 ANKRD30BL, GPR39, LYPD1, NCKAP5 Transgenic mice Enhancer Forebrain, midbrain, hindbrain, spinal cord Gain of function Brain development [37]
2xHAR.170 chr5:153640309–153640363 GALNT10, SAP30L, HAND1 Transgenic mice Enhancer Isthmus and spinal cord Loss and gain of function Brain development [37]
HAR25 chr4:182271922–182272882 ODZ3 Transgenic mice Enhancer Eye Loss of function Eye development [37]
ANC705 chr15:61,979,891–61,980,090 VPS13C, RORA Epigenetic marks Enhancer Neural crest Gain of function Neural crest development [44]
HAR89; 2xHAR.305 chr1:3,089,780–3,089,980 PRDM16 Epigenetic marks Enhancer Neural crest Gain of function (chimp) Neural crest development [44]
2xHAR.236 chr1:53,992,480–53,992,679 GLIS1 Epigenetic marks ENHANCER Neural crest Gain of function (chimp) Neural crest development [44]
HACNS825 chr2:217,728,749–217,728,948 TNP1; LOC105373876 Epigenetic marks ENHANCER Neural crest Gain of function (chimp) Neural crest development [44]
2xHAR87 chr11:115648183–115648526 CADM1 Epigenetic marks and 4-C ENHANCER Cerebellum Gain of function compared to macaque Synapse regulation [43]
DAR-12/HACNS219 chr5:158227696–158229500 RNF145 Luciferase ENHANCER SK-N-MC cells Gain of function Hematological traits [38]
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