Table 1.

All Significant and Suggestive HLOD Scores From Variant Based Linkage

CHR	rsID	POS	HLOD	GENE	FUNC	EXON	FREQ	SIFT	POLYPH	FATHMM	CADD	REVEL
7	rs4719841	25997536	4.34	MIR148A; NFE2L3	Intergenic	.	0.27	.	.	.	.	.
7	rs235397	35372749	3.42	LOC401324	ncRNA	.	0.20	.	.	.	.	.
7	rs6462100	28754095	3.01	CREB5	Intronic	.	0.40	.	.	.	.	.
7	rs7797330	30895010	2.84	INMT-MINDY4	ncRNA	.	0.38	.	.	.	.	.
7	rs7779240	27562660	2.82	EVX1; HIBADH	Intergenic	.	0.15	.	.	.	.	.
20	rs3746736	23424613	2.75	CSTL1	Exonic	nonsyn	0.20	T	B	T	0.003	0.086
9	rs10757225	21555445	2.73	MIR31HG	ncRNA	.	0.18	.	.	.	.	.
2	rs1920511	41792845	2.59	SLC8A1; LINC01913	Intergenic	.	0.33	.	.	.	.	.
7	rs10270663	34786398	2.58	NPSR1-AS1	ncRNA	.	0.20	.	.	.	.	.
7	rs1427483	33959239	2.49	BMPER	Intronic	.	0.29	.	.	.	.	.
9	rs61757558	117118379	2.48	AKNA	Exonic	nonsyn	0.06	D	B	T	22.6	0.019
7	rs2270219	31877261	2.42	PDE1C	Intronic	.	0.23	.	.	.	.	.
7	rs3735400	36438709	2.40	ANLN	Exonic	nonsyn	0.12	D	D	T	29.7	0.204
7	rs6462088	28504566	2.40	CREB5	Intronic	.	0.24	.	.	.	.	.
7	rs2011974	32611392	2.35	AVL9	Intronic	.	0.34	.	.	.	.	.
6	rs214950	152708310	2.29	SYNE1	Exonic	nonsyn	0.15	D	B	T	7.324	0.104
7	rs10266620	31957550	2.29	PDE1C	Intronic	.	0.26	.	.	.	.	.
1	rs7550997	26596080	2.27	CEP85	Exonic	nonsyn	0.18	T	B	T	15.09	0.043
1	rs8564	26605069	2.27	CEP85	UTR3	.	0.18	.	.	.	.	.
1	rs7544	26607726	2.27	SH3BGRL3	UTR3	.	0.18	.	.	.	.	.
1	rs10493030	26561856	2.27	CEP85	Intronic	.	0.18	.	.	.	.	.
1	rs10902732	26606174	2.27	SH3BGRL3; CEP85	Intergenic		0.18	.	.	.	.	.
1	rs11247900	26612460	2.27	UBXN11	Exonic	syn	0.18	.	.	.	.	.
1	rs11577318	26601570	2.27	CEP85	Intronic	.	0.18	.	.	.	.	.
1	rs17163746	26564230	2.27	CEP85	Intronic	.	0.18	.	.	.	.	.
1	rs17163749	26568165	2.26	CEP85	Intronic	.	0.18	.	.	.	.	.
10	rs61729846	5920244	2.26	ANKRD16	Exonic	nonsyn	0.20	D	D	T	26.1	0.690
18	rs387462	3458997	2.26	TGIF1	downstream	.	0.36	.	.	.	.	.
7	rs6952967	31795856	2.24	PDE1C	Intronic	.	0.47	.	.	.	.	.
6	rs791183	160610124	2.23	SLC22A1; SLC22A2	Intergenic	.	0.40	.	.	.	.	.
7	rs1420123	29647662	2.16	PRR15; LOC646762	Intergenic	.	0.27	.	.	.	.	.
7	rs1029602	24571485	2.15	NPY; MPP6	Intergenic	.	0.38	.	.	.	.	.
7	rs4291168	31178749	2.14	ADCYAP1R1; NEUROD6	Intergenic	.	0.18	.	.	.	.	.
20	rs6036107	22403287	2.13	LOC284788; LINC00261	Intergenic	.	0.33	.	.	.	.	.
1	rs2228579	1223385	2.13	SCNN1D	Exonic	nonsyn	0.33	T	B	T	0.003	0.036
6	rs34544438	167438292	2.12	FGFR1OP	Exonic	nonsyn	0.07	T	B	T	0.268	0.119
7	rs1285407	9266388	2.11	NXPH1; PER4	Intergenic	.	0.12	.	.	.	.	.
7	rs12113424	35423720	2.11	LOC401324; HERPUD2	Intergenic	.	0.19	.	.	.	.	.
2	rs13424561	73868446	2.11	NAT8	Exonic	nonsyn	0.11	T	B	T	0.166	0.01
3	rs36117895	11400019	2.10	ATG7	Exonic	nonsyn	0.12	D	P	T	25.3	0.227
9	rs10511687	20764870	2.10	FOCAD	Exonic	nonsyn	0.32	T	B	T	14.75	0.069
7	rs6415258	32192596	2.10	PDE1C	Intronic	.	0.27	.	.	.	.	.
7	rs212837	26695215	2.08	C7orf71; SKAP2	Intergenic	.	0.35	.	.	.	.	.
1	rs12138111	26590432	2.07	CEP85	Intronic	.	0.19	.	.	.	.	.
18	rs77600482	3460731	2.06	TGIF1; GAPLINC	Intergenic	.	0.15	.	.	.	.	.
9	rs10973446	37638744	2.05	TOMM5; FRMPD1	Intergenic	.	0.45	.	.	.	.	.
18	rs381234	3464650	2.02	TGIF1; GAPLINC	Intergenic	.	0.38	.	.	.	.	.
7	rs731844	34150264	2.02	BMPER	Intronic	.	0.39	.	.	.	.	.
5	rs7715811	13769974	2.01	DNAH5	Intronic	.	0.39	.	.	.	.	.
5	rs1502050	13779743	2.01	DNAH5	Intronic	.	0.38	.	.	.	.	.
7	rs10224983	34180326	1.98	BMPER	Intronic	.	0.15	.	.	.	.	.
7	rs961652	34111660	1.95	BMPER	Intronic	.	0.30	.	.	.	.	.
7	rs16480	24311069	1.95	STK31; NPY	Intergenic	.	0.38	.	.	.	.	.
7	rs2033670	22929061	1.94	SNHG26; FAM126A	Intergenic	.	0.33	.	.	.	.	.
10	rs7071768	129903016	1.93	MKI67	Exonic	nonsyn	0.47	T	B	T	0.001	0.022
1	rs10908292	36764770	1.92	THRAP3	Intronic	.	0.39	.	.	.	.	.
20	rs5741809	36956026	1.92	BPI	Exonic	nonsyn	0.14	T	B	T	0.001	0.011
7	rs2392246	33571828	1.91	BBS9	Intronic	.	0.12	.	.	.	.	.
7	rs976681	24530016	1.91	NPY; MPP6	Intergenic	.	0.36	.	.	.	.	.

The list of all significant and suggestive variants from the variant-based linkage analyses, as sorted by HLOD. Here, the headers represent: CHR = chromosome, rsID = rsID of the SNP, POS = physical position in base pairs of the SNP, HLOD = heterogeneity LOD score across all 106 families, GENE = Gene location of the SNP (if intergenic then the two closest genes), FUNC = function of the SNP (e.g. exonic, intronic), EXON = if exonic, the exonic function of the SNP (nonsyn = nonsynonymous, syn = synonymous), FREQ = frequency of the variant in gnomAD Africans, SIFT = SIFT prediction (T = tolerated, D = damaging), POLY = PolyPhen2 prediction score (B = benign, P = possibly damaging, D = damaging), FATHMM = FATHMM prediction (T = tolerated), CADD = CADD phred score ≥ 10 corresponds to 10% most deleterious substitutions in genome, ≥ 20 corresponds to 1% most deleterious substitutions in the genome, etc.), REVEL = REVEL score (corresponds to proportion of trees in random forest algorithm that classified variant as pathogenic).