Table 2 Sequences that were cloned for functional validation.

From: Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus

Common SNP ID

Ref.

DNA sequence with variant site (underlined and capitalized)

Gene Implicated

Variant 1 (Var1)

Variant 2 (Var2)

rs9888739

17

GGTTCCATCTTCCCTGTTCAtattctttcCcaccatagccacctgagaccatctagttttctggcctctggtctctgggtttttgctagccttacatttttctttctttatgtttaaaaatttttttattgtggtaagggcacttaacatgagacctatcctcttaacagattttaaaatgtacaatgtaatactgtcatctaTTGGTGCAATGTTGTACAGC

ITGAM

C

G

rs10488631

52

TGTACAGGGAACCCCTTGTCctctccctgagctggGtgtgggtttgcaaggagacatgtgacccagaccaaccctgggagcagcagggcgcctgctgtctggccactcttactaggactgctgtGgcacttcctcccctagtgggtccctggtgcccatgaattgcagctcctgggtggtggtgggggcACTGTCTCCTG GGACTCCAG

IRF5

Var1

Var2

Var3

Var4

GG

GA

AG

AA

rs3823536

35

CAGGTACCAAAGGCTGCTTCcatagctagtctagctgaacCatttccgagctacaaggcagtgaatgaaagtaaaaacaaagaaacactggttaaattttaaaaatttattctttctcttttgttgctgttgatttgttcttgagatggctacaacacCAGACAGAACAGTGCCCTCA

IRF5

C

A

rs12574073

39

GGCCCTGTTGTGTGATACCTtctgacacatacgtttttttgaaaaaagattgtctgctgggaactggactgaaaccaacatataacCgtttgtttcatactggttaggaagccaccaggaaggcctacccaaagtggttttaaatacatacacacacagtcctctcctctTAGAGCCAAGAACAGGCCAT

ETS1

C

T

rs10036748

35

CAGCATGGTGTGACCAAATCacagCgggtacaggagtaaaacagtaaccagtgggttggagagagaggcagacaaacaacctcctacaacgctgcctctctcaaatcaggtcggcctgacccaaccaggacatccgggccccaagtcacaggcagcactgggggtaagggtatgactcagaccccacagcttcctggggccccgaAAAAACTGGTGGGGGTATCC

TNIP1

C

G

rs5754217

53

Sequence forward:

GGCAAGTCACTGGCTTCTTC

Sequence reverse: CAAGGAAGCCAAATTGAGGA

UBE2L3

Insertion

rs969985

9

Sequence forward: CAGCAGCCAGAGCTTACTGA

Sequence reverse: ACAGCCAACACTGATTGCAC

BLK

Insertion

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