Variant report

Variant	rs9818758
Chromosome Location	chr3:49382925-49382926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49382380-49383039	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49382322-49383116	HUVEC	blood vessel:	n/a	n/a
3	MTA3	chr3:49382327-49383118	GM12878	blood:	n/a	n/a
4	NFATC1	chr3:49382372-49382973	GM12878	blood:	n/a	n/a
5	PAX5	chr3:49382446-49383034	GM12878	blood:	n/a	chr3:49382881-49382890
6	FOXM1	chr3:49382250-49382986	GM12878	blood:	n/a	n/a
7	BCLAF1	chr3:49382345-49383048	GM12878	blood:	n/a	n/a
8	STAT5A	chr3:49382392-49383000	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr3:49382456-49382962	GM12878	blood:	n/a	n/a
10	TAF1	chr3:49382439-49382961	GM12878	blood:	n/a	n/a
11	CREB1	chr3:49382472-49382955	GM12878	blood:	n/a	n/a
12	NFIC	chr3:49382262-49383064	GM12878	blood:	n/a	n/a
13	ELF1	chr3:49382451-49382990	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49382468-49382955	GM12878	blood:	n/a	n/a
15	RUNX3	chr3:49382345-49383045	GM12878	blood:	n/a	n/a
16	YY1	chr3:49382502-49382966	GM12878	blood:	n/a	n/a
17	IKZF1	chr3:49382443-49383051	GM12878	blood:	n/a	n/a
18	NFIC	chr3:49382321-49383082	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49382413-49382959	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:49382454-49382983	GM12891	blood:	n/a	n/a
21	BATF	chr3:49382433-49382955	GM12878	blood:	n/a	chr3:49382719-49382728
22	TAF1	chr3:49382534-49382937	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:49382447-49383371	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:49382363-49383003	GM12892	blood:	n/a	n/a
25	JUN	chr3:49382485-49382927	HUVEC	blood vessel:	n/a	n/a
26	FOS	chr3:49382502-49382936	HUVEC	blood vessel:	n/a	n/a
27	ATF2	chr3:49382376-49383064	GM12878	blood:	n/a	n/a
28	EP300	chr3:49382462-49382935	GM12878	blood:	n/a	chr3:49382876-49382890
29	CHD1	chr3:49382524-49382964	GM12878	blood:	n/a	n/a
30	STAT3	chr3:49382511-49382955	GM12878	blood:	n/a	n/a
31	MTA3	chr3:49382422-49383036	GM12878	blood:	n/a	n/a
32	SPI1	chr3:49382333-49382946	GM12891	blood:	n/a	n/a
33	REST	chr3:49382434-49382957	HL-60	blood:	n/a	n/a
34	ATF2	chr3:49382367-49383018	GM12878	blood:	n/a	n/a
35	IRF4	chr3:49382456-49382987	GM12878	blood:	n/a	n/a
36	TCF3	chr3:49382521-49382973	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:49382522-49382996	GM12878	blood:	n/a	n/a
38	NFATC1	chr3:49382396-49382937	GM12878	blood:	n/a	n/a
39	WRNIP1	chr3:49382562-49382955	GM12878	blood:	n/a	n/a
40	SP1	chr3:49382451-49382930	GM12878	blood:	n/a	n/a
41	BCLAF1	chr3:49382429-49382989	GM12878	blood:	n/a	n/a
42	RELA	chr3:49382540-49382950	GM15510	blood:	n/a	n/a
43	RUNX3	chr3:49382356-49383035	GM12878	blood:	n/a	n/a
44	EP300	chr3:49382481-49382942	GM12878	blood:	n/a	chr3:49382876-49382890
45	SPI1	chr3:49382369-49383011	HL-60	blood:	n/a	n/a
46	POU2F2	chr3:49382452-49383029	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:49382411-49383060	HL-60	blood:	n/a	n/a
48	FOXM1	chr3:49382333-49383065	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:49382338-49383100	HL-60	blood:	n/a	n/a
50	PML	chr3:49382279-49383039	GM12878	blood:	n/a	chr3:49382884-49382892

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49377677..49379380-chr3:49380905..49382983,2	K562	blood:

Variant related genes	Relation type
USP4	TF binding region
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10049462	0.93[MKK][hapmap];1.00[YRI][hapmap]
rs11707940	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709788	0.85[ASN][1000 genomes]
rs11713297	0.82[YRI][hapmap]
rs11719220	0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs11920251	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11922013	1.00[CHB][hapmap]
rs12497569	0.83[ASN][1000 genomes]
rs12715435	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13068038	0.93[MKK][hapmap];1.00[YRI][hapmap]
rs13077498	0.85[CHD][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs13077723	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13078949	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1865741	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2230929	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304442	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs34142492	0.81[ASN][1000 genomes]
rs34366700	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34514189	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34567776	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34915642	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35060561	0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs35446411	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35869135	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410472	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4554002	0.81[ASN][1000 genomes]
rs4955431	0.83[ASN][1000 genomes]
rs56038006	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67485053	0.82[ASN][1000 genomes]
rs67882627	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6795772	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73086105	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7640903	0.81[ASN][1000 genomes]
rs9311440	0.89[YRI][hapmap]
rs9837625	0.82[YRI][hapmap]
rs9839368	1.00[YRI][hapmap]
rs9844757	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9863142	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864406	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9874474	0.91[EUR][1000 genomes]
rs9883409	0.91[EUR][1000 genomes]
rs9990153	0.82[YRI][hapmap]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9818758	NICN1	cis	cerebellum	SCAN
rs9818758	C3orf62	cis	parietal	SCAN
rs9818758	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9818758	UQCRC1	cis	parietal	SCAN
rs9818758	GPX1	cis	parietal	SCAN
rs9818758	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9818758	NBEAL2	cis	cerebellum	SCAN
rs9818758	RNF123	cis	parietal	SCAN
rs9818758	C3orf62	cis	cerebellum	SCAN
rs9818758	CELSR3	cis	cerebellum	SCAN
rs9818758	NDUFAF3	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49383800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:49378600-49383800	Weak transcription	NHEK	skin
3	chr3:49378600-49384000	Weak transcription	NHLF	lung
4	chr3:49378600-49384200	Weak transcription	HSMMtube	muscle
5	chr3:49378600-49384400	Weak transcription	Psoas Muscle	Psoas
6	chr3:49378600-49385200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:49378600-49386400	Weak transcription	K562	blood
8	chr3:49378600-49386600	Weak transcription	Stomach Mucosa	stomach
9	chr3:49378600-49386800	Weak transcription	Gastric	stomach
10	chr3:49378600-49388400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:49378600-49388800	Weak transcription	Brain Substantia Nigra	brain
12	chr3:49378600-49388800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:49378600-49390000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:49378800-49383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:49378800-49383800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:49378800-49384000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:49378800-49384200	Enhancers	Adipose Nuclei	Adipose
19	chr3:49378800-49386800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:49378800-49387400	Weak transcription	Esophagus	oesophagus
21	chr3:49379000-49383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49379000-49384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:49379000-49385800	Weak transcription	Fetal Intestine Large	intestine
24	chr3:49379000-49385800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
26	chr3:49379400-49384000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:49379600-49384000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:49379600-49384200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:49379600-49384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:49379800-49386600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
32	chr3:49380400-49385800	Enhancers	Placenta	Placenta
33	chr3:49381200-49383400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:49381200-49384800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:49381200-49384800	Enhancers	HepG2	liver
36	chr3:49381400-49383000	Enhancers	Fetal Thymus	thymus
37	chr3:49381400-49383800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:49381400-49388800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:49381600-49383000	Enhancers	Spleen	Spleen
40	chr3:49381600-49383600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
42	chr3:49381800-49384600	Enhancers	HUVEC	blood vessel
43	chr3:49382000-49383000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:49382000-49383200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:49382000-49383200	Enhancers	NHDF-Ad	bronchial
46	chr3:49382000-49383400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:49382000-49384000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:49382200-49383200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49382200-49384000	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:49382200-49384200	Weak transcription	Fetal Muscle Trunk	muscle

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