Table 1 17q21.31 haplotype- and sub-haplotype-defining SNVs. SNV alleles observed on: GRCh38 direct orientation haplotype H1 or sub-haplotype H1.2_b (GRCh38-NC_000017.11); GRCh38 direct orientation sub-haplotype H1.2_e (GRCh38-NT_187663.1); GRCh38 inverted orientation H2.1 (from Steinberg et al. [18], no reference assembly was included in the original paper); and GRCh38 inverted orientation haplotype H2 or sub-haplotype H2D (GRCh38-NT_167251.2). SNV genomic coordinates and annotated gene are shown. Amino acid positions are based on the following isoform references: CRHR1: NP_001289945.1, SPPL2C: NP_787078.2, MAPT: NP_058519.3, STH: NP_001007533.1, KANSL1: NP_001180395.1, NSF: NP_006169.2. Bold text denotes non-synonymous SNVs predicted to cause amino acid substitutions

rs241039

LINC02210-CRHR1

-

45,637,307

A

T

[20]

rs393152

LINC02210-CRHR1

-

45,641,777

A

G

[32]

rs434428

LINC02210-CRHR1

-

45,648,318

G

A

[20]

rs241027

LINC02210-CRHR1

-

45,658,112

A

G

[20]

rs2049515

LINC02210-CRHR1

-

45,684,490

C

T

[20]

rs10491144

LINC02210-CRHR1

-

45,695,758

A

C

[20]

rs10514879

LINC02210-CRHR1

-

45,725,605

C

T

[20]

rs2902662

LINC02210-CRHR1

-

45,729,559

G

A

[20]

rs17563599

LINC02210-CRHR1

-

45,730,589

A

C

[18]

rs11079718

LINC02210-CRHR1

-

45,762,585

A

T

[20]

rs1396862

CRHR1

intron variant

45,825,631

G

A

[20]

rs16940681

CRHR1

E280Q

45,834,793

G

C

[33]

rs62621252

SPPL2C

S224P

45,845,576

T

C

[33]

rs62054815^a

SPPL2C

A332T

45,845,900

G

A

[33]

rs12185233^a

SPPL2C

R461P

45,846,288

G

C

[33]

rs12185268^a

SPPL2C

I471V

45,846,317

A

G

[33]

rs12373123^a

SPPL2C

S601P

45,846,707

T

C

[33]

rs12373139^a

SPPL2C

G620R

45,846,764

G

A

[33]

rs12373142

SPPL2C

P643R

45,846,834

C

G

[33]

rs1078830

MAPT-AS1

-

45,868,746

T

C

[20]

rs916793

MAPT-AS1

-

45,877,320

G

A

[20]

rs1467967^b

MAPT

intron variant

45,908,813

G

A

A

A

[29, 34]

rs17563986

MAPT

intron variant

45,913,906

A

G

[18]

rs17649553

MAPT

intron variant

45,917,282

C

T

[35]

rs242557^b

MAPT

intron variant

45,942,346

G

G

A

G

[27]

rs17650901

MAPT

5' UTR variant

45,962,325

A

G

[20]

rs1800547

MAPT

intron variant

45,974,480

A

G

[16]

rs17651213

MAPT

intron variant

45,974,558

G

A

[20]

rs3785883^b

MAPT

intron variant

45,977,067

A

G

G

G

[29, 34]

rs1981997

MAPT

intron variant

45,979,401

G

A

[18]

rs63750417

MAPT

P202L

45,983,409

C

T

[33]

rs62063786

MAPT

D285N

45,983,657

G

A

[33]

rs62063787

MAPT

V289A

45,983,670

T

C

[33]

rs17651549

MAPT

R370W

45,983,912

C

T

[33]

rs10445337

MAPT

S447P

45,990,034

T

C

[33]

rs1052553

MAPT

P544P

45,996,523

A

G

[20]

rs2471738^b

MAPT

intron variant

45,998,697

C

C

T

C

[27]

rs62063857

STH

Q7R

45,999,299

A

G

[33]

rs8070723

MAPT

intron variant

46,003,698

A

G

[18, 36, 37]

rs9468

MAPT

3'UTR variant

46,024,197

T

C

[16, 38]

rs7521^b

MAPT

3'UTR variant

46,028,029

A

A

G

G

[29, 34]

rs34579536

KANSL1

I1085T

46,031,540

A

G

[33]

rs36076725

KANSL1

F917L

46,033,166

G

A

[11]

rs35833914

KANSL1

D914E

46,033,175

G

A

[11]

rs34043286

KANSL1

S718P

46,039,753

A

G

[33]

rs12150447

KANSL1

intron variant

46,050,759

A

C

[20]

rs2838

KANSL1

intron variant

46,063,981

A

G

[20]

rs1468241

KANSL1

intron variant

46,118,787

A

G

[20]

rs1528075

KANSL1

intron variant

46,143,088

T

G

[20]

rs1528072

KANSL1

intron variant

46,159,359

C

A

[20]

rs1881193

KANSL1

R247S

46,171,403

T

C

[33]

rs2732703

ARL17B and LRRC37A

intron variants

46,275,856

T

G

[39]

rs2957297

ARL17B and LRRC37A

intron variants

46,290,846

C

G

[18]

rs199457^c

LRRC37A2 and NSF

intron variants

46,718,103

C

C

T

[18]

rs199456^c

LRRC37A2 and NSF

intron variants

46,720,553

C

C

T

[18]

rs199451^c

LRRC37A2 and NSF

intron variants

46,724,418

G

G

A

[18]

rs199448^c

LRRC37A2 and NSF

intron variants

46,731,635

A

A

G

[18]

rs199533^c

NSF

K702K

46,751,565

G

G

A

[18]