. 2014 Sep 17;26(3):692–714. doi: 10.1681/ASN.2014010028

Table 3.

Summary of the CRATs correlating with eGFR

CKD Risk-Associated Locus	Location (Chromosome)	Position	Genes within ±250 kb	CRATs Correlating with eGFR in T and G Samples	Position of the SNP Relative to Each Correlating CRAT	No. of Total Correlating CRATs (P<0.05)
rs267734	1	150951477	CTSS^b^,^e	CTSS (T and G)^f	Upstream	8
			CTSK^b^,^e	CTSK (T^f and G)	Upstream
			ARNT^b^,^e	CERS2 (T)^f	Upstream
			SETDB1^b^,^e	ANXA9 (T^f and G)	Downstream
			CERS2^a^,^e	PRUNE (T^f)	Downstream
			ANXA9^a^,^e	MLLT11 (T)	Downstream
			FAM63A^a^,^e	CDC42SE1 (T)	Downstream
			PRUNE^a^,^e	PIP5K1A (T)^f	Downstream
			MLLT11^b^,^e
			BNIPL^c
			C1orf56^b^,^e
			GABPB2^b
			SEMA6C^b^,^e
			CDC42SE1^a^,^e
			LYSMD1^b
			SCNM1^b^,^e
			TMOD4^c
			VPS72^a^,^e
			PIP5K1A^a^,^e
			TNFAIP8L2^c^,^e
rs1933182	1	109999588	SARS^a^,^e	PSRC1 (G)	Upstream	4
			CELSR2^b^,^e	SORT1 (T and G)	Upstream
			PSRC^c^,^e	GNAI3 (T^f)	Downstream
			MYBPHL^c	GSTM4 (T^f)	Downstream
			SORT1^a^,^e
			PSMA5^a^,^e
			SYPL2^a
			ATXN7L2^b
			CYB561D1^b
			AMIGO1^b
			GPR61^c
			GNAI3^a^,^e
			AMPD2^b^,^e
			GSTM2^a^,^e
			GSTM4^a^,^e
			GSTM1^a^,^e
			GNAT2^c^,^e
rs12124078	1	15869899	FHAD1^c	EFHD2 (G)	Upstream	8
			EFHD2^a^,^e	CELA2A (T)	Upstream
			CTRC^d^,^e	CELA2B (T)	Upstream
			CELA2A^d^,^e	CASP9 (T^f and G)	Upstream
			CELA2B^c^,^e	DNAJC16 (T^f)	Intronic
			CASP9^a^,^e	AGMAT (T^f and G)	Downstream
			DNAJC16^a^,^e	DDI2 (T^f)	Downstream
			AGMAT^a^,^e	RSC1A1 (T^f)	Downstream
			DDI2^b^,^e
			RSC1A1^b^,^e
			SLC25A34^b
			TMEM82^a
			FBLIM1^a
rs16864170	2	5907880	SOX11^c^,^e	SOX11 (T^f)	Upstream	1
rs6431731	2	15863002	DDX1^a^,^e	DDX1 (T)	Upstream	2
rs6431731			MYCN^b^,^e	MYCN (T^f and G)	Downstream
rs10206899	2	73900900	ALMS1^b^,^e	NAT8 (T^f)	Upstream	2
			NAT8^a^,^e	NAT8B (T^f)	Downstream
			NAT8B^a^,^e
			TPRKB^a^,^e
			DUSP11^a^,^e
			C2orf78^c
			STAMBP^b^,^e
			ACTG2^c^,^e
rs7583877	2	100460654	AFF3^c^,^e	AFF3 (T^f)	Intronic	1
rs347685	3	141807137	ATP1B3^a^,^e	TFDP2 (T^f)	Intronic	1
			TFDP2^b^,^e
			GK5^b
			XRN1^b
rs17319721	4	77368847	SCARB2^a^,^e	FAM47E (T^f and G^f)	Upstream	2
rs13146355		77412140	FAM47E^b^,^e	STBD1 (T^f and G^f)	Upstream
			STBD1^b^,^e
			CCDC158^c
			SHROOM3^b
rs6420094	5	176817636	NSD1^b^,^e	NSD1 (T^f)	Upstream	7
			RAB24^a	SLC34A1 (T^f and G)	Intronic
			PRELID1^a	F12 (G)	Downstream
			MXD3^c^,^e	GRK6 (T^f)	Downstream
			LMAN2^a^,^e	DBN1 (T)	Downstream
			RGS14^a^,^e	PDLIM7 (T)	Downstream
			SLC34A1^a^,^e	FAM193B (T^f)	Downstream
			PFN3^b
			F12^b^,^e
			GRK6^b^,^e
			PRR7^c^,^e
			DBN1^a^,^e
			PDLIM7^a^,^e
			DOK3^c^,^e
			DDX41^a^,^e
			FAM193B^b^,^e
			TMED9^a^,^e
			B4GALT7^a^,^e
rs11959928	5	39397132	FYB^b^,^e	FYB (T^f and G^f)	Upstream	2
			C9^c^,^e	DAB2 (T^f)	Intronic
			DAB2^a^,^e
rs881858	6	43806609	POLH^b^,^e	VEGFA (T^f and G)	Upstream	1
			GTPBP2^a^,^e
			MAD2L1BP^a^,^e
			RSPH9^c
			MRPS18A^a^,^e
			VEGFA^a^,^e
			C6orf223^c
rs2279463	6	160668389	IGF2R^a^,^e	IGF2R (T^f)	Upstream	4
			SLC22A1^c^,^e	SLC22A1 (T^f)	Upstream
			SLC22A2^a^,^e	SLC22A2 (T^f)	Intronic
			SLC22A3^b^,^e	SLC22A3 (G)	Downstream
rs3828890	6	31440669	HLA-C^a^,^e	HLA-C (G)	Upstream	8
			HLA-B^a^,^e	MICB (T^f and G)	Downstream
			MICA^b^,^e	LST1 (T^f and G)	Downstream
			MICB^c^,^e	NCR3 (T^f)	Downstream
			DDX39B^a^,^e	AIF1 (T^f)	Downstream
			ATP6V1G2^b^,^e	BAG6 (T^f)	Downstream
			LTA^c^,^e	APOM (T^f)	Downstream
			NFKBIL1^a^,^e	LTB (T^f and G^f)	Downstream
			LST1^b^,^e
			NCR3^c^,^e
			AIF1^a^,^e
			PRRC2A^a^,^e
			BAG6^a^,^e
			C6orf47^a^,^e
			GPANK1^b
			CSNK2B^a^,^e
			LY6G5B^b
			ABHD16A^a
			LY6G5C^b^,^e
			APOM^a^,^e
			LY6G6F^d
			LY6G6C^c^,^e
			DDAH2^a^,^e
			C6orf25^c^,^e
			LTB^b^,^e
			TNF^c^,^e
rs6465825	7	77416439	PTPN12^a^,^e	PTPN12 (T)	Upstream	3
			RSBN1L^b	PHTF2 (T^f)	Downstream
			TMEM60^a	MAGI2 (G)	Downstream
			PHTF2^b^,^e
			MAGI2^b^,^e
rs7805747	7	151407801	RHEB^a^,^e			0
rs7805747			PRKAG2^a^,^e
rs10277115	7	1285195	C7orf50^a	GPER (T^f)	Upstream	2
			GPR146^b	MICALL2 (G^f)	Downstream
			GPER^b^,^e
			ZFAND2A^a
			UNCX^c
			MICALL2^b^,^e
			INTS1^a^,^e
rs1617640	7	100317298	TSC22D4^a^,^e	LRCH4 (T^f and G)	Upstream	4
			NYAP1^c	PCOLCE (G)	Upstream
			AGFG2^b^,^e	SLC12A9 (T)	Downstream
			SAP25^b^,^e	TRIP6 (T^f)	Downstream
			LRCH4^a^,^e
			FBXO24^c^,^e
			PCOLCE^b^,^e
			MOSPD3^a^,^e
			TFR2^c^,^e
			ACTL6B^d^,^e
			GNB2^a^,^e
			GIGYF1^b
			POP7^a^,^e
			EPO^b^,^e
			ZAN^d
			EPHB4^a^,^e
			SLC12A9^a^,^e
			TRIP6^a^,^e
			SRRT^a^,^e
			UFSP1^b
			ACHE^c^,^e
rs10109414	8	23751151	NKX3-1^c^,^e	STC1 (T^f)	Upstream	1
rs1731274		23766319	NKX2-6^d
rs1731274			STC1^a^,^e
rs4744712	9	71434707	PIP5K1B^b^,^e			0
			FAM122A^b
			PRKACG^d^,^e
			FXN^b^,^e
rs10794720	10	1156165	LARP4B^b^,^e	LARPB4 (T^f)	Upstream	2
			GTPBP4^a^,^e	IDI1 (T)	Upstream
			IDI2^b^,^e
			IDI1^a^,^e
			WDR37^b^,^e
			ADARB2^c^,^e
rs4014195	11	65506822	SCYL1^a	LTBP3 (T^f)	Upstream	11
			LTBP3^a^,^e	FAM89B (T^f)	Upstream
			SSSCA1^a^,^e	EHBP1L1 (T^f and G^f)	Upstream
			FAM89B^a^,^e	SIPA1 (T^f)	Upstream
			EHBP1L1^b^,^e	RELA (T)	Upstream
			KCNK7^c^,^e	CFL1 (T)	Downstream
			MAP3K11^a^,^e	CCDC85B (T^f)	Downstream
			PCNXL3^b	FOSL1 (T^f)	Downstream
			SIPA1^b^,^e	CTSW (T^f)	Downstream
			RELA^a^,^e	FIBP (T^f)	Downstream
			KAT5^a^,^e	DRAP1 (G)	Downstream
			RNASEH2C^a
			AP5B1^b
			OVOL1^b^,^e
			SNX32^c
			CFL1^a^,^e
			MUS81^a^,^e
			EFEMP2^a^,^e
			CCDC85B^a^,^e
			FOSL1^b^,^e
			CTSW^c^,^e
			FIBP^a^,^e
			C11orf68^a^,^e
			TSGA10IP^d
			SART1^a^,^e
			DRAP1^a^,^e
rs3925584	11	30760335	MPPED2^b^,^e	MPPED2 (T^f)	Upstream	1
			DCDC5^c
			DCDC1^c
rs653178	12	112007756	CUX2^c^,^e	CUX2 (T)	Upstream	4
			FAM109A^b	ATXN2 (T^f)	Intronic
			SH2B3^b^,^e	ACAD10 (T^f)	Downstream
			ATXN2^b^,^e	ALDH2 (T^f)	Downstream
			BRAP^b^,^e
			ACAD10^a^,^e
			ALDH2^a^,^e
rs10774021	12	349298	IQSEC3^b^,^e	SLC6A12 (T^f)	Upstream	3
			SLC6A12^a^,^e	SLC6A13 (T^f and G)	Intronic
			SLC6A13^a^,^e	KDM5A (G)	Downstream
			KDM5A^b^,^e
			CCDC77^b
			B4GALNT3^b
rs626277	13	72347696	DACH1^b^,^e	DACH1 (T)	Intronic	1
rs491567	15	53946593	WDR72^a			0
rs1394125	15	76158983	SNUPN^a^,^e			0
			IMP3^a^,^e
			SNX33^b
			CSPG4^c^,^e
			ODF3L1^c
			UBE2Q2^a
			NRG4^c
			C15orf27^c
rs2453533	15	45641225	DUOX1^c^,^e	DUOX1 (T^f)	Upstream	4
			DUOXA2^c	SLC28A2 (T)	Upstream
			DUOXA1^d	GATM (T^f and G)	Downstream
			SHF^c	SLC30A4 (T^f)	Downstream
			SLC28A2^b^,^e
			GATM^a^,^e
			SPATA5L1^b^,^e
			C15orf48^b
			SLC30A4^b^,^e
			BLOC1S6^a
rs12437854	15	94141833	No gene in <250 kb distance			0
rs12917707	16	20367690	GP2^b^,^e	GP2 (T and G)	Upstream	6
rs4293393		20364588	UMOD^a^,^e	UMOD (T^f and G)	Upstream
rs11864909		20400839	PDILT^d	ACSM5 (T^f and G)	Downstream
			ACSM5^a^,^e	ACSM2A (T^f)	Downstream
			ACSM2A^a^,^e	ACSM2B (T^f)	Downstream
			ACSM2B^a^,^e	ACSM1 (T)	Downstream
			ACSM1^c^,^e
rs9895661	17	59456589	BCAS3^b^,^e	TBX2 (T^f)	Downstream	1
			TBX2^a^,^e
			C17orf82^c
			TBX4^d^,^e
			NACA2^b^,^e
rs2453580	17	19438321	EPN2^b^,^e	EPN2 (T)	Upstream	4
			B9D1^a^,^e	MFAP4 (T^f and G^f)	Upstream
			MAPK7^b^,^e	SLC47A1 (T^f)	Intronic
			MFAP4^a^,^e	ALDH3A2 (T^f and G)	Downstream
			RNF112^c
			SLC47A1^a^,^e
			ALDH3A2^a^,^e
			ALDH3A1^c^,^e
			SLC47A2^a
			ULK2^b^,^e
rs11078903	17	37631924	FBXL20^b	ERBB2 (T^f)	Downstream	1
			MED1^b^,^e
			CDK12^b^,^e
			NEUROD2^d^,^e
			PPP1R1B^b
			STARD3^a^,^e
			PNMT^c^,^e
			PGAP3^a^,^e
			ERBB2^a^,^e
			TCAP^c^,^e
rs7208487	17	37543449	PLXDC1^c^,^e	PLXDC1 (T^f and G)	Upstream	1
			CACNB1^c^,^e
			ARL5C^d
			RPL19^a^,^e
			STAC2^b
			FBXL20^b
			MED1^b^,^e
			CDK12^b^,^e
			NEUROD2^d^,^e
			PPP1R1B^b
			STARD3^a^,^e
rs12460876	19	33356891	ANKRD27^b^,^e	SLC7A9 (T^f)	Intronic	1
			RGS9BP^c
			NUDT19^b^,^e
			TDRD12^c^,^e
			SLC7A9^a^,^e
			CEP89^b
			C19orf40^c^,^e
			RHPN2a
			GPATCH1^b^,^e
rs911119	20	23612737	NAPB^b	CST8 (T)	Upstream	1
rs13038305		23610262	CSTL1^d
			CST11^c^,^e
			CST8^c^,^e
			CST9L^d
			CST9^c
			CST3^a^,^e
			CST4^d^,^e
			CST1^d^,^e
			CST2^d^,^e
			CST5^c^,^e
rs6040055	20	10633313	MKKS^a^,^e	MKKS (T)	Upstream	1
			SLX4IP^c
			JAG1^a^,^e
rs4821469	22	36616445	APOL3^a^,^e	MYH9 (T)	Downstream	1
			APOL4^b
			APOL2^a^,^e
			APOL1^a^,^e
			MYH9^a^,^e
			TXN2^a^,^e

The table shows the list of genes within the 250-kb region of the CKD-associated SNPs. Baseline expression of the transcripts in human kidneys (by RNA sequencing) are shown. T, tubule; G, glomerular.

High expression.

Medium expression.

Low expression.

No expression.

Genes with available probe set identifications on the microarray chip.

The correlation with eGFR in T and G samples remained significant (P<0.05) after Benjamini-Hochberg multiple testing correction.