Spreadsheet: 4bbc6f29-c23b-4c53-83ba-62e5c23fd4a2
Sheet: Table S1

Table S1. AUTS2 enhancer candidates (AECs) selected for enhancer assays
AEC # | Chromosomal position (hg18) | Location | Conservation ǂ | Forebrain/Midbrain p300 ChIP-Seq peak ǂǂ | Human-Neanderthal conservation* | Zebrafish enhancer? | Tissue ** | [NAME]? ◊ | Tissue ◊◊ | Forward Primer | Reverse primer | [NAME] (bp)
1 | chr7:68,724,902-68,728,333 | Sweep | Chicken | Midbrain P300 | (D,D,D,D,D,D,D) | No | Negative | Not Tested |  | GGGTAGAAAGAACTGCCTTGATT | GGCTTCCACATCTGACAGTAGAC | 3246
2 | chr7:68,812,867-68,814,245 | Sweep | Chicken | Midbrain p300 | (DD,D) | No | Negative | Not Tested |  | CCCTTTTTAGTTTCTTCCCTTCA | TACAAAGCACCTGCTCTTTTCTC | 1444
3 | chr7:68,821,855-68,823,820 | Sweep, dyslexia non-coding deletion ([NAME] et al., [NAME] (2011) 7: e1002334) | Chicken | Midbrain p300 | (D,DDD) | Yes | Dots around caudal end of tail in somite area (18%, 24hpf) | Not Tested |  | ACCCCAGCCACTTAGTTTTGTA | ACCTAGTAAACGCTGTTGTCCTG | 1966
4 | chr7:68,825,835-68,827,626 | Sweep, dyslexia non-coding deletion ([NAME] et al., [NAME] (2011) 7: e1002334) | Opossum |  | (DDDDD,D,D) | Yes | Notochord (31%, 24hpf; 30%, 48hpf) Otic vesicle (16%, 24hpf; 28%, 48hpf) | Not Tested |  | GAAAACATGATCATTTCCAGGAG | CAATGATCACTAAGAGAGTTTGTGG | 1792
5 | chr7:68,841,424-68,843,440 | Sweep, dyslexia non-coding deletion ([NAME] et al., [NAME] (2011) 7: e1002334) | Frog | Midbrain p300 | (D,D,D,D) | Yes | Midbrain (39%, 24hpf; 27%, 48hpf) Somitic Muscle plus dots at end of tail (60%, 24hpf) Otic vesicle (15%, 48hpf) Somitic Muscle (16%, 48hpf) | Not Tested |  | CCCTCTCCCCAGCTGATATT | TTCTGATTTAAGTATGTTTTTGTCAAG | 2017
6 | chr7:68,875,482-68,877,048 | Sweep, dyslexia non-coding deletion ([NAME] et al., [NAME] (2011) 7: e1002334) | [NAME] |  | (D,D,D,D,D,DDD,DDDD,D) | Yes | Pericardium (29%, 24hpf; 34%, 48hpf) Eye (28%, 48hpf) | Not Tested |  | AGTGACTTGGACTACAGGCACAT | ACATCTTTGCTTAGCAGGCAGTA | 1567
7 | chr7:68,908,734-68,909,828 | Sweep | Dog |  | (DDD,D,DDDD,D), | No | Negative | Not Tested |  | ATTTAGGCAGCAGTGACAGAAAG | CCAAATCTGATGAAGAGTCCAAC | 1095
8 | chr7:68,922,864-68,924,172 | Sweep | [NAME] |  | (DDDDD,D,D) | No | Negative | Not Tested |  | AAGTATGAGCCAGTCTTGAGGTG | TGAAAAACTTACTGGACTTAAATGTG | 1309
9 | chr7:68,928,408-68,929,934 | Sweep | [NAME] | Forebrain p300 | (D,D,D,DDD) | No | Negative | Not Tested |  | [NAME] | GCCAAATGCCTAATAAAGACAGA | 1527
10 | chr7:68,963,804-68,965,620 | Sweep, HACNS369 | Opossum |  | (D,D,D,DDDD) | Yes | Midbrain (60%, 24hpf; 58%, 48hpf), [NAME] all over mostly above notochord (55%, 24hpf; 39%, 48hpf)  Spinal cord (18%, 48hpf) | Yes | Midbrain (12/13, E12.5) Eye (6/13, E12.5) Proximal limb (6/13, E12.5) | GGAGGCTACTTTTCCTCTGAAAG | CAAGTCACCTTTAAGCTTCCTTCT | 1817
11 | chr7:68,966,890-68,968,624 | Sweep | Chicken | Mid/forebrain p300 | (D) | No | Negative | Not Tested |  | CTCTCTGACAGACCTGTGACTTG | TACACACAGGGGTTAAAAAGGAA | 1735
12 | chr7:68,996,372-68,998,072 | Sweep | Opossum | Midbrain p300 | (D,D,D,D,D) | Yes | Epidermis (59%, 24hpf; 50%, 48hpf) Forebrain (39% 24hpf; 34%, 48hpf) Heart (15%, 24hpf) Otic Vesicle (24%, 24hpf; 34%, 48hpf) | Not Tested |  | ACTTGACAGACCAAAATGACAGG | TGACTACATGCCTGTGTAATTGTTT | 1701
13 | chr7:69,036,983-69,038,688 | Sweep | [NAME] |  | (D,D) | Yes | Otic Vesicle (19%, 48hpf) | Yes (hs 1660) | Ear (5/8, E11.5) | GAAAACAGTTAGCTGCGGAATCT | TCTGGGTACAAACTTCACACTGA | 1706
14 | chr7:69,108,779-69,109,947 | Sweep | Zebrafish |  | (D,D,D) | Yes | [NAME] (18%, 24hpf) | Not Tested |  | TTATGTGCATGTTCCAAAGTTTTT | TAAGGATAAACAGCCCTGTGAAA | 1229
15 | chr7:69,166,208-69,168,337 | Sweep | Chicken | Midbrain p300 | (DD,D,D,DDDD,D,D,D,D,D,D) | Yes | Eye (19%, 48hpf) | Not Tested |  | ATGGGTTTTGGGTTTTGTTTTT | GCTGACAAAGTTTTGTGGTTTTT | 2116
16 | chr7:69,183,577-69,186,403 | Sweep | Opossum | Midbrain p300 | (D,D,D,D,D,DD) | Yes | Ventral Caudal region (25%, 24hpf; 26%, 48hpf) | Not Tested |  | CCAAATGAGAATGTAGCTCTGTG | TATGCTATATGGGTGCAATTTTT | 2777
17 | chr7:69,195,062-69,196,938 | Sweep | Zebrafish |  | (D,D,D) | No | Negative | Not Tested |  | TCACCAGTACATTTTTATTCCTTCC | TGAGCATCTGTGCATCTAAAGTG | 1877
18 | chr7:69,200,457-69,202,216 | Sweep | Zebrafish |  | (D,D,D) | Yes | Spots on top or end of tail (18%, 24hpf) | Not Tested |  | ATCAGAGATTGTTTGGAGAGCAT | GAGTGCAAGAAAATCTGCCTTTA | 1818
19 | chr7:69,206,936-69,208,600 | Sweep | Zebrafish |  | (DD,D,D,D,DDDD,D) | Yes | Heart (42%, 24hpf; 33%, 48hpf) Hindbrain (23%, 24hpf)  [NAME] (38%, 48hpf) | Not Tested |  | CAAAAATGAAAGCAGCTTAATGG | GGAGAGGCCAGTAAATGAAGAGT | 1721
20 | chr7:69,217,233-69,219,228 | Sweep | Opossum | Midbrain p300 | (D,D,D,D,DDDDD) | Yes | Midbrain (22%, 24hpf) | Not Tested |  | GATGCTCATACAAATCAATGCAA | ATCATCCTTTCCAGAAATTCACC | 1996
21 | chr7:69,234,838-69,236,265 | Sweep | Zebrafish |  | (DDD,D) | Yes | [NAME] (15%, 48hpf) | Yes (hs 1425) | Midbrain (4/6, E11.5) | TCTTGGGGTTGTAGGACTAGACA | TGTAAGAAAAATGGCTCAGGAGA | 1428
22 | chr7:69,236,069-69,238,171 | Sweep, includes exon | Zebrafish |  | (D,DD,D,D) | No | Negative | Not Tested |  | GATCACACATCTATGGTGCTTCA | TGAAAAGGGTCACTAAATCCAGA | 2175
23 | chr7:69,274,050-69,276,432 | Sweep boarder | Zebrafish |  | (D,DD,D,D,D) | Yes | [NAME] (50%, 24hpf; 47%, 48hpf) | Not Tested |  | TGTCTCATGGAGAAATCCTCATT | AATATGCCAGATGCTGTTTCTGT | 2411
24 | chr7:69,284,310-69,286,965 | HAR31 | Chicken |  | (D,D,DDD,D,D,D,D,D,D) | Yes | Hindbrain (17%, 24hpf) Spinal cord (66%, 24hpf; 31%, 48hpf) | Yes | Eye (4/5, E11.5) | AACAGGCAAATTCTGTTGTAGGA | ATTTTCCTCTATGACCTGCCTTC | 2656
25 | chr7:69,312,912-69,316,619 | Between sweep and ASD non-coding deletion | Zebrafish |  | (D,D,D,D,D,D,D) | Yes | Blood islands-yolk (18%, 24hpf) | Not Tested |  | CAAATGACATTGGGGTATAGGAA | TAGCAAGAGCCATCGTTTTAGAG | 3654
26 | chr7:69,316,920-69,317,888 | Between sweep and ASD non-coding deletion | Opossum | Midbrain p300 | (D,D) | Yes | Forebrain (45%, 24hpf; 40%, 48hpf) Otic Vesicle (23%, 48hpf) | Not Tested |  | AAGGTAACTGCAGCACTTTTGAA | GAGCTTGCAGTCTTGGAAACTT | 969
27 | chr7:69,340,167-69,341,551 | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Zebrafish | Midbrain P300 | (D,D,D) | Yes | [NAME] (30%, 48hpf) | Yes (hs 658) | Midbrain (11/15, E11.5)  Neural tube (9/15, E11.5) | CCAGAACTTGAACCTTGCATCT | GGCAAGGAGGAGACATAAAATG | 1385
28 | chr7:69,343,769-69,346,450 | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Zebrafish |  | (D,D,D,DDD,D,D,D) | No | Negative | Not Tested |  | ACTCACCACCACAAGTCAGAAAT | GGTTAGCCTGAGTAAAACCCTGT | 2715
29 | chr7:69,358,340-69,359,796 | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Frog |  | (D,D,DDDDD,D) | Yes | Forebrain (olfactory organ) (15%, 48hpf) Heart (23%, 48hpf) | Yes | Olfactory epithelium (3/6, E12.5) Eye (6/6, E12.5) | CTTTTTCTGTGGTGTTCCTTTTG | CCCTTAGCTCTACACCAGACTGA | 1410
30 | [NAME] | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Frog |  | (D,D,D) | No | Negative | Not Tested |  | GGCCTTCCTTACAGGTCTAATTG | AAACTTCGTAAGAAAATGGCAAA | 2920
31 | chr7:69,365,749-69,367,561 | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Frog |  | (D,D,D) | No | Negative | Not Tested |  | GGCCACAGTAGAGTCATGATGTT | CCCAGTGAAAAGGACAATAACAG | 1781
32 | chr7:69,369,740-69,372,052 | ASD non-coding deletion ([NAME], [NAME] (2010) 466: 368-72) | Zebrafish |  | (D,DDDDD,D) | Yes | Midbrain (19%, 48hpf) Hindbrain (18%, 48hpf) | Yes | Midbrain (4/4, E12.5) Forebrain (4/4, E12.5) Hindbrain (4/4, E12.5) Eye (4/4, E12.5) | CTTTGACTTAACGAGAGCCTGAG | AGCAAATCTGGGTTAAGGATGAT | 2262
33 | chr7:69,374,313-69,375,754 | To end of intron 4 | Zebrafish |  | (D,D,D,D) | No | Negative | Not Tested |  | CAGCAGTGCTACCTTTCTACCTC | TGTCTTTCTAGAGACGTTTTCTTTACC | 1442
34 | chr7:69,439,813-69,441,520 | To end of intron 4, epilepsy non-coding deltion ([NAME] et al., [NAME] genetics (2010)6: e1000962) | Zebrafish |  |  | No | Negative | Not Tested |  | GAAGCTTACTTACCTGCCTTGGT | AATTTCTTCTGGGCTTTAACTGG | 1708
35 | chr7:69,443,563-69,444,772 | To end of intron 4, epilepsy non-coding deltion ([NAME] et al., [NAME] genetics (2010)6: e1000962),  alcohol consumption SNP ([NAME], PNAS (2011), 108: 7119-24) | Zebrafish |  | (D) | No | Negative | Not Tested |  | AAGGTCAGCATCCTCAGTACAAA | TGCACTGCAAGTCAATAAGTTGT | 1210
36 | chr7:69,456,365-69,457,073 | To end of intron 4, epilepsy non-coding deltion ([NAME] et al., [NAME] genetics (2010)6: e1000962) | Frog | Midbrain P300 |  | Yes | Hindbrain (18%, 24hpf) | Not Tested |  | CAAATATCACACAGGAGACCTTTC | GACAGGGACAGGAATGTACTGAG | 709
37 | chr7:69,458,163-69,460,029 | To end of intron 4, epilepsy non-coding deltion ([NAME] et al., [NAME] genetics (2010)6: e1000962) | Zebrafish | Forebrain p300 | (D,DD,D,D,D,D,D,D) | No | Negative | Not Tested |  | TTCCAGAAATCCGACAGAAAGTA | CTTCCCACTTAGAGCCCAACTAC | 1867
38 | chr7:69,479,431-69,480,094 | To end of intron 4 | [NAME] | Midbrain P300 | (D,D,D) | Yes | Epidermis, only on head (24%, 24hpf) | Not Tested |  | ATATCCTGGGTGGGCATGAGTAT | CTTTAGGCTTCAAAGAAGCATGG | 664
39 | chr7:69,534,927-69,536,470 | To end of intron 4 | Fugu |  | (DD,D,D,D,D) | No | Negative | Not Tested |  | CTGTGATTGCTGTAAGGCCTAGT | GAAGACTTTGAAGGCCTAGAACC | 1544
40 | chr7:69,654,802-69,656,119 | HACNS174 | Frog |  | (DD,D) | No | Negative | Not Tested |  | AAAGGGAAAACCACCATCACTAC | TAAAATACGCACAGGGTCTGTCT | 1318
ǂ Comparative genomics carried out using the ECR browser (http://ecrbrowser.dcode.org/) with the following parameters: ≥70% identity for at least 100bp.
ǂǂ EP300 ChIP-Seq data taken from [NAME] et al., [NAME], 854-8 (2009)
* "D" represents the derived status of a SNP. A red SNPS means that at least four of the six modern human genomes are derived. Additional Information regarding human-Neanderthal SNPs can be found here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=226193491&c=chr7&g=ntSssSnps
** Zebrafish tissue data: the tissues specific expression of sequences positive for enhancer activity are mentioned along with the percent positive of total alive fish after subtracting out the empty vector followed by the hours post fertilization (hpf) of expression.
◊ Mouse enhancer data for (hs 1425), (hs 658) and (hs 1660) were aquired from the VISTA enhancer browser: http://enhancer.lbl.gov/
◊◊ Mouse tissue data: the tissue specific expression of the sequences positive for enhancer activity out of the total LacZ stained mice along with the embryonic day (E) that they were assayed at.