Variant report

Variant	rs3813346
Chromosome Location	chr6:133561646-133561647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr6:133561438-133562090	A549	lung:	n/a	chr6:133562055-133562065
2	MAX	chr6:133561411-133564645	Hela-S3	cervix:	n/a	chr6:133563073-133563082 chr6:133562175-133562185
3	USF2	chr6:133561531-133561894	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:133561597-133563777	HEK293	kidney:	n/a	n/a
5	POLR2A	chr6:133561626-133561837	A549	lung:	n/a	n/a
6	POLR2A	chr6:133561511-133561995	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:133561483-133562168	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr6:133561520-133563623	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr6:133561485-133564625	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr6:133561420-133562153	ECC-1	luminal epithelium:	n/a	n/a
11	SIN3A	chr6:133561635-133562127	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr6:133561457-133563236	ECC-1	luminal epithelium:	n/a	chr6:133563073-133563082 chr6:133562175-133562185
13	MXI1	chr6:133561597-133561893	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr6:133561345-133562103	Hela-S3	cervix:	n/a	n/a
15	CHD2	chr6:133561606-133564777	Hela-S3	cervix:	n/a	chr6:133562178-133562188
16	KAP1	chr6:133561422-133562080	HEK293	kidney:	n/a	n/a
17	BRCA1	chr6:133561423-133562630	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:133561613-133561937	A549	lung:	n/a	n/a
19	POLR2A	chr6:133561537-133564670	Hela-S3	cervix:	n/a	n/a
20	MAX	chr6:133561468-133562100	A549	lung:	n/a	n/a
21	MXI1	chr6:133561495-133564967	IMR90	lung:	n/a	n/a
22	ZNF143	chr6:133561634-133562098	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr6:133561574-133564470	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr6:133561546-133563551	A549	lung:	n/a	n/a
25	MXI1	chr6:133561492-133562878	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr6:133561566-133562154	Hela-S3	cervix:	n/a	n/a
27	MAX	chr6:133561436-133563623	A549	lung:	n/a	chr6:133563073-133563082 chr6:133562175-133562185
28	POLR2A	chr6:133561569-133562217	Hela-S3	cervix:	n/a	n/a
29	MAZ	chr6:133561591-133563676	Hela-S3	cervix:	n/a	chr6:133563073-133563082 chr6:133562175-133562185
30	POLR2A	chr6:133561560-133562141	U87	brain:	n/a	n/a
31	EP300	chr6:133561502-133564863	ECC-1	luminal epithelium:	n/a	chr6:133564793-133564807 chr6:133562188-133562197 chr6:133562216-133562225
32	POLR2A	chr6:133561606-133562845	A549	lung:	n/a	n/a
33	ZKSCAN1	chr6:133561614-133562129	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:133561623-133561815	A549	lung:	n/a	n/a
35	MAZ	chr6:133561537-133564291	IMR90	lung:	n/a	chr6:133563073-133563082 chr6:133562175-133562185
36	RFX5	chr6:133561534-133562172	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:133561610-133562148	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr6:133561563-133563111	ECC-1	luminal epithelium:	n/a	n/a
39	SP1	chr6:133561580-133562183	A549	lung:	n/a	n/a
40	SMC3	chr6:133561569-133564559	Hela-S3	cervix:	n/a	n/a
41	KAP1	chr6:133561531-133562077	U2OS	brain:	n/a	n/a
42	CTCF	chr6:133561644-133562966	A549	lung:	n/a	chr6:133562171-133562184 chr6:133561790-133561803 chr6:133561992-133562005
43	MAFK	chr6:133561492-133562088	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr6:133561523-133562587	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr6:133561580-133562106	Hela-S3	cervix:	n/a	chr6:133562004-133562017 chr6:133561995-133562005 chr6:133561589-133561599
46	MAX	chr6:133561436-133562909	A549	lung:	n/a	chr6:133562175-133562185
47	POLR2A	chr6:133561484-133562021	H1-neurons	neurons:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:133561614-133561664	SKMC	muscle:	n/a
2	chr6:133561614-133561664	HNPCEpiC	eye:	n/a
3	chr6:133561630-133561680	ovcar-3	ovarian:	n/a
4	chr6:133561630-133561680	SK-N-SH	brain:	n/a
5	chr6:133561630-133561680	GM06990	blood:	n/a
6	chr6:133561630-133561680	HepG2	liver:	n/a
7	chr6:133561630-133561680	ProgFib	skin:	n/a
8	chr6:133561630-133561680	GM12891	blood:	n/a
9	chr6:133561630-133561680	Caco-2	colon:	n/a
10	chr6:133561630-133561680	SK-N-SH_RA	brain:	n/a
11	chr6:133561614-133561664	CMK	blood:	n/a
12	chr6:133561614-133561664	IMR90	lung:	fetal
13	chr6:133561614-133561664	AG04449	skin:	fetal
14	chr6:133561614-133561664	PFSK-1	brain:	n/a
15	chr6:133561630-133561680	HCF	heart:	n/a
16	chr6:133561614-133561664	GM12878	blood:	n/a
17	chr6:133561630-133561680	ECC-1	luminal epithelium:	n/a
18	chr6:133561630-133561680	HCT-116	colon:	n/a
19	chr6:133561630-133561680	RPTEC	kidney:	n/a
20	chr6:133561630-133561680	HUVEC	blood vessel:	n/a
21	chr6:133561614-133561664	Hela-S3	cervix:	n/a
22	chr6:133561614-133561664	LNCaP	prostate:	n/a
23	chr6:133561630-133561680	Hela-S3	cervix:	n/a
24	chr6:133561614-133561664	HCT-116	colon:	n/a
25	chr6:133561614-133561664	HCF	heart:	n/a
26	chr6:133561614-133561664	HEK293	kidney:	embryo
27	chr6:133561614-133561664	NHDF-neo	bronchial:	n/a
28	chr6:133561630-133561680	IMR90	lung:	fetal
29	chr6:133561614-133561664	HAEpiC	amniotic membrane:	n/a
30	chr6:133561614-133561664	GM06990	blood:	n/a
31	chr6:133561630-133561680	Hepatocyte	liver:	n/a
32	chr6:133561614-133561664	HRCEpiC	kidney:	n/a
33	chr6:133561614-133561664	GM19239	blood:	n/a
34	chr6:133561614-133561664	HPAEpiC	pulmonary alveolar:	n/a
35	chr6:133561630-133561680	NHBE	bronchial:	n/a
36	chr6:133561630-133561680	U87	brain:	n/a
37	chr6:133561630-133561680	NH-A	brain:	n/a
38	chr6:133561630-133561680	AG10803	skin:	n/a
39	chr6:133561614-133561664	SK-N-SH	brain:	n/a
40	chr6:133561614-133561664	SK-N-MC	brain:	n/a
41	chr6:133561614-133561664	HCPEpiC	choroid plexus:	n/a
42	chr6:133561630-133561680	MCF-7	breast:	n/a
43	chr6:133561630-133561680	AG09319	gingival:	n/a
44	chr6:133561630-133561680	MCF10A-Er-Src	breast:	n/a
45	chr6:133561614-133561664	HUVEC	blood vessel:	n/a
46	chr6:133561630-133561680	CMK	blood:	n/a
47	chr6:133561614-133561664	SK-N-SH_RA	brain:	n/a
48	chr6:133561630-133561680	NHDF-neo	bronchial:	n/a
49	chr6:133561630-133561680	HNPCEpiC	eye:	n/a
50	chr6:133561614-133561664	RPTEC	kidney:	n/a

No data

Variant related genes	Relation type
EYA4	TF binding region
EYA4	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1338009	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1361147	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361148	0.84[ASN][1000 genomes]
rs1361149	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038476	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756867	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777787	0.80[ASN][1000 genomes]
rs4895955	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4895959	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569872	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903443	0.81[ASN][1000 genomes]
rs7775273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321391	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758080	chr6:133444719-133627364	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2759470	chr6:133444719-133627364	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv470862	chr6:133492507-133600402	Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv886678	chr6:133550279-133631190	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv5483	chr6:133554303-133599338	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3813346	EYA4	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133560800-133562000	Bivalent Enhancer	Fetal Heart	heart
2	chr6:133561400-133561800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
3	chr6:133561400-133561800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr6:133561400-133561800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr6:133561400-133561800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr6:133561400-133563400	Bivalent/Poised TSS	Fetal Lung	lung
7	chr6:133561400-133563600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:133561400-133564000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:133561400-133564400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:133561400-133564600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:133561400-133564800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:133561400-133565200	Active TSS	HSMMtube	muscle
13	chr6:133561400-133565400	Active TSS	Hela-S3	cervix
14	chr6:133561400-133565800	Active TSS	A549	lung
15	chr6:133561400-133566400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:133561600-133561800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr6:133561600-133561800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:133561600-133561800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
19	chr6:133561600-133561800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:133561600-133561800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:133561600-133561800	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
22	chr6:133561600-133561800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr6:133561600-133561800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr6:133561600-133561800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:133561600-133561800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:133561600-133561800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:133561600-133561800	Bivalent Enhancer	Adipose Nuclei	Adipose
28	chr6:133561600-133561800	Bivalent Enhancer	Liver	Liver
29	chr6:133561600-133561800	Bivalent Enhancer	Brain Anterior Caudate	brain
30	chr6:133561600-133561800	Active TSS	Brain Hippocampus Middle	brain
31	chr6:133561600-133561800	Bivalent Enhancer	Esophagus	oesophagus
32	chr6:133561600-133561800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr6:133561600-133561800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
34	chr6:133561600-133561800	Bivalent Enhancer	Placenta	Placenta
35	chr6:133561600-133561800	Bivalent Enhancer	Fetal Stomach	stomach
36	chr6:133561600-133561800	Flanking Bivalent TSS/Enh	NH-A	brain
37	chr6:133561600-133561800	Bivalent/Poised TSS	NHDF-Ad	bronchial
38	chr6:133561600-133561800	Flanking Active TSS	NHLF	lung
39	chr6:133561600-133562000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:133561600-133562000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:133561600-133562000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:133561600-133562000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:133561600-133562000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
44	chr6:133561600-133562000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr6:133561600-133562200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr6:133561600-133562400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:133561600-133562400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr6:133561600-133562400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:133561600-133562400	Bivalent Enhancer	Fetal Brain Male	brain
50	chr6:133561600-133562400	Active TSS	Pancreas	Pancrea

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