Variant report

Variant	rs13077498
Chromosome Location	chr3:49313978-49313979
allele	C/T
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	chr3:49313891-49315337	GM12891	blood:	n/a	n/a
2	MAX	chr3:49313833-49314314	H1-hESC	embryonic stem cell:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
3	POU2F2	chr3:49313925-49314830	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:49313815-49315390	GM12892	blood:	n/a	n/a
5	CEBPB	chr3:49313957-49314613	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49313870-49315078	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr3:49313706-49315442	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:49313935-49314902	H1-hESC	embryonic stem cell:	n/a	n/a
9	RUNX3	chr3:49313789-49314834	GM12878	blood:	n/a	n/a
10	RUNX3	chr3:49313793-49314908	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:49313785-49314858	U87	brain:	n/a	n/a
12	NFATC1	chr3:49313836-49315065	GM12878	blood:	n/a	n/a
13	PML	chr3:49313557-49315281	GM12878	blood:	n/a	chr3:49315192-49315201
14	E2F6	chr3:49313720-49314926	H1-hESC	embryonic stem cell:	n/a	chr3:49314767-49314777
15	MAX	chr3:49313862-49314847	SK-N-SH	brain:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
16	POLR2A	chr3:49313905-49314838	GM12878	blood:	n/a	n/a
17	MAX	chr3:49313749-49314907	ECC-1	luminal epithelium:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
18	WRNIP1	chr3:49313972-49314317	GM12878	blood:	n/a	n/a
19	MAX	chr3:49313881-49314175	NB4	blood:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
20	POLR2A	chr3:49313830-49314999	HL-60	blood:	n/a	n/a
21	MAX	chr3:49313810-49314255	H1-hESC	embryonic stem cell:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
22	POLR2A	chr3:49313929-49313996	K562	blood:	n/a	n/a
23	TAF1	chr3:49313847-49314813	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr3:49313897-49314852	U87	brain:	n/a	n/a
25	BCL3	chr3:49313923-49314904	GM12878	blood:	n/a	chr3:49314526-49314539
26	BCLAF1	chr3:49313894-49314905	GM12878	blood:	n/a	chr3:49314526-49314539
27	YY1	chr3:49313835-49314491	H1-hESC	embryonic stem cell:	n/a	chr3:49314463-49314471
28	MAZ	chr3:49313736-49315010	IMR90	lung:	n/a	n/a
29	POLR2A	chr3:49313819-49315176	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:49313762-49314985	GM12891	blood:	n/a	n/a
31	MAX	chr3:49313754-49314956	A549	lung:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
32	CREB1	chr3:49313957-49314885	GM12878	blood:	n/a	n/a
33	BCLAF1	chr3:49313848-49314959	GM12878	blood:	n/a	chr3:49314526-49314539
34	MTA3	chr3:49313432-49315520	GM12878	blood:	n/a	n/a
35	STAT5A	chr3:49313506-49314877	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:49313890-49315407	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr3:49313778-49314950	GM12891	blood:	n/a	n/a
38	ELF1	chr3:49313882-49314863	GM12878	blood:	n/a	chr3:49314522-49314534
39	POLR2A	chr3:49313656-49315136	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:49313884-49314862	K562	blood:	n/a	n/a
41	POLR2A	chr3:49313749-49314837	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:49313827-49315159	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr3:49313553-49315014	HL-60	blood:	n/a	n/a
44	POLR2A	chr3:49313767-49315147	PFSK-1	brain:	n/a	n/a
45	MXI1	chr3:49313960-49314230	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:49313878-49315082	GM12892	blood:	n/a	n/a
47	POLR2A	chr3:49313529-49315539	GM12878	blood:	n/a	n/a
48	MAX	chr3:49313844-49314946	ECC-1	luminal epithelium:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
49	POLR2A	chr3:49313757-49315463	GM12878	blood:	n/a	n/a
50	MTA3	chr3:49313727-49314935	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49313590..49315716-chr3:49315985..49318300,2	MCF-7	breast:

Variant related genes	Relation type
C3orf62	TF binding region
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10154895	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865954	1.00[JPT][hapmap]
rs11130184	1.00[JPT][hapmap]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11710247	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715581	1.00[JPT][hapmap]
rs11716445	0.92[CEU][hapmap]
rs11718982	0.81[EUR][1000 genomes]
rs11719220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11720460	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12490393	1.00[JPT][hapmap]
rs12493001	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12493284	0.81[ASN][1000 genomes]
rs12629637	0.94[ASN][1000 genomes]
rs12629759	1.00[JPT][hapmap]
rs12631989	1.00[JPT][hapmap]
rs12637576	1.00[JPT][hapmap]
rs12715434	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096406	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13321689	1.00[ASW][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs3212	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs34326553	0.82[EUR][1000 genomes]
rs34343820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34566463	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34784192	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34915642	0.85[CHD][hapmap]
rs35060561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35174559	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35185152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4279134	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4410472	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4513485	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4521268	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955410	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955419	1.00[JPT][hapmap]
rs4955420	1.00[JPT][hapmap]
rs4955432	1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs56306491	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66991555	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67286839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6779394	1.00[JPT][hapmap]
rs67831908	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71324939	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73084135	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7614738	0.80[ASN][1000 genomes]
rs7626445	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7638154	0.84[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311440	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9814987	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9818758	0.85[CHD][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9826085	1.00[ASW][hapmap]
rs9826525	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835439	0.87[EUR][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9840050	0.85[CHD][hapmap]
rs9844757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9847839	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9850917	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9855123	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9862483	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9863142	0.85[CHD][hapmap]
rs9864406	0.85[CHD][hapmap]
rs9870030	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9873994	0.85[CHD][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9874474	0.83[ASN][1000 genomes]
rs9880088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883409	0.83[ASN][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs13077498	HEMK1	cis	parietal	SCAN
rs13077498	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs13077498	C3orf62	cis	cerebellum	SCAN
rs13077498	NICN1	cis	cerebellum	SCAN
rs13077498	RNF123	cis	parietal	SCAN
rs13077498	WDR6	cis	cerebellum	SCAN
rs13077498	WDR6	cis	Adipose Subcutaneous	GTEx
rs13077498	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13077498	WDR6	cis	Artery Tibial	GTEx
rs13077498	WDR6	cis	Esophagus Mucosa	GTEx
rs13077498	CCDC36	cis	cerebellum	SCAN
rs13077498	WDR6	cis	parietal	SCAN
rs13077498	CSPG5	cis	parietal	SCAN
rs13077498	ARIH2	cis	cerebellum	SCAN
rs13077498	KBTBD3	trans	parietal	SCAN
rs13077498	ALAS1	cis	cerebellum	SCAN
rs13077498	LRRC2	cis	cerebellum	SCAN
rs13077498	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49301800-49315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49303600-49315600	Weak transcription	HepG2	liver
3	chr3:49304800-49314000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:49307200-49314000	Weak transcription	Esophagus	oesophagus
5	chr3:49307200-49314200	Weak transcription	Hela-S3	cervix
6	chr3:49307400-49314000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:49307400-49314000	Weak transcription	Gastric	stomach
8	chr3:49307400-49314600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:49307400-49314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:49307600-49314000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:49309000-49314000	Weak transcription	Lung	lung
12	chr3:49309200-49316000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:49310800-49314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:49311800-49315200	Weak transcription	K562	blood
15	chr3:49312600-49314000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:49313200-49314000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:49313200-49314000	Enhancers	Pancreas	Pancrea
19	chr3:49313200-49318600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:49313200-49349400	Strong transcription	Dnd41	blood
22	chr3:49313400-49314000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:49313400-49314000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:49313400-49314000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:49313400-49314000	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:49313400-49314000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:49313400-49314000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49313400-49314000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:49313400-49314000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:49313400-49314000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:49313400-49314000	Enhancers	Small Intestine	intestine
32	chr3:49313400-49314000	Enhancers	HSMM	muscle
33	chr3:49313400-49314000	Enhancers	HSMMtube	muscle
34	chr3:49313400-49314200	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr3:49313400-49314400	Flanking Active TSS	Fetal Heart	heart
36	chr3:49313400-49314400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:49313400-49314400	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:49313400-49318600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:49313600-49314000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:49313600-49314000	Enhancers	Liver	Liver
41	chr3:49313600-49314000	Enhancers	Colonic Mucosa	Colon
42	chr3:49313600-49314000	Flanking Active TSS	Fetal Brain Female	brain
43	chr3:49313600-49314000	Flanking Active TSS	Fetal Kidney	kidney
44	chr3:49313600-49314000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:49313600-49314000	Enhancers	HMEC	breast
46	chr3:49313600-49314000	Enhancers	NHEK	skin
47	chr3:49313600-49314200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:49313600-49314200	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr3:49313600-49314200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr3:49313600-49314200	Flanking Active TSS	Rectal Smooth Muscle	rectum

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