TABLE 1.

All lncRNA regions where SNPs with p < 10^–5 were found.

Regions	Position	Subject of the region	Subject associated gene	Subject position	Subject rationale	FANTOM-CAT gene category based on DHS support (DHS support in paranthesis)	FANTOM-CAT gene class based on coding potential and genomic context
lncRNA-45	chr3:177484653-177667012	ENSG000 00231574	RP11-91K9.1	chr3:177534653-177617012	LncRNA expression positively correlates with a BC high/moderate penetrance gene expression	e-lncRNA (enhancer)	lncRNA, intergenic
lncRNA-49	Chr6:33167311-33272766	ENSG00 000232940		chr4:33217311-33222766	LncRNA expression positively correlates with a BC high/moderate penetrance gene expression	others (dyadic)	lncRNA, divergent
lncRNA-103	chr8:17689552-17790170	ENSG00 000253215		chr8:17739552-17740170	LncRNA expression positively correlates with a BC high/moderate penetrance gene expression	others (no)	ncRNA, divergent
lncRNA-26	chr10:38403576-38551285	ENSG00 000224761	RP11-508N22.8	chr10:38453576-38501285	LncRNA higly expressed in breast tumor tissue	not in FANTOM-CAT db	not in FANTOM-CAT db
lncRNA-82	chr11:18571334-18681802	ENSG000 00247595	RP11-504G3.1	chr11:18621334-18631802	LncRNA moderately expressed in breast tumor tissue and its expression positively correlates with RAD50 expression	p-lncRNA (promoter)	lncRNA, divergent
lncRNA-17	chr14:101195747-101377368	ENSG00 000214548	MEG3	chr14:101245747-101327368	LncRNA higly expressed in breast tumor tissue	p-lncRNA (promoter)	lncRNA, intergenic
lncRNA-75	chr15:50597156-50714399	ENSG0000 0244879	GABPB1-AS1	chr15:50646371-50650503	LncRNA expression positively correlates with BRCA1 expression	p-lncRNA (promoter)	lncRNA, divergent