Variant report

Variant	rs13074291
Chromosome Location	chr3:89156519-89156520
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	MAX	chr3:89156502-89157028	A549	lung:	n/a	n/a
2	TAF1	chr3:89156512-89156956	PFSK-1	brain:	n/a	n/a
3	ZNF143	chr3:89156484-89157124	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOSL1	chr3:89156501-89156865	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr3:89156517-89156905	A549	lung:	n/a	chr3:89156613-89156623 chr3:89156611-89156625
6	PAX5	chr3:89156488-89156828	GM12892	blood:	n/a	chr3:89156675-89156694
7	POLR2A	chr3:89156444-89157084	SK-N-MC	brain:	n/a	n/a
8	MAX	chr3:89156516-89156730	GM12878	blood:	n/a	n/a
9	PAX5	chr3:89156489-89156866	GM12878	blood:	n/a	chr3:89156675-89156694
10	POLR2A	chr3:89156474-89157103	PFSK-1	brain:	n/a	n/a
11	TAF1	chr3:89156462-89157018	PFSK-1	brain:	n/a	n/a
12	ZNF263	chr3:89156412-89157334	HEK293-T-REx	kidney:	n/a	n/a
13	GATA2	chr3:89156495-89157117	SH-SY5Y	brain:	n/a	chr3:89156760-89156770 chr3:89156761-89156768 chr3:89156761-89156770 chr3:89156762-89156779
14	SIN3AK20	chr3:89156477-89157088	H1-hESC	embryonic stem cell:	n/a	n/a
15	SETDB1	chr3:89156244-89157181	U2OS	brain:	n/a	n/a
16	SIN3A	chr3:89156516-89157179	H1-hESC	embryonic stem cell:	n/a	chr3:89156559-89156573
17	MAX	chr3:89156460-89157288	ECC-1	luminal epithelium:	n/a	n/a
18	MYC	chr3:89156412-89157048	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr3:89156463-89157290	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr3:89156481-89156985	H1-hESC	embryonic stem cell:	n/a	chr3:89156641-89156654 chr3:89156879-89156889 chr3:89156877-89156889
21	MXI1	chr3:89156498-89157174	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXP2	chr3:89156493-89157001	PFSK-1	brain:	n/a	chr3:89156503-89156515
23	FOSL1	chr3:89156419-89156967	H1-hESC	embryonic stem cell:	n/a	chr3:89156420-89156429
24	MAX	chr3:89156466-89157241	MCF-7	breast:	n/a	n/a
25	E2F6	chr3:89156498-89157188	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr3:89156519-89156831	GM12878	blood:	n/a	chr3:89156658-89156665
27	ZNF143	chr3:89156297-89156926	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:89156334-89157193	SK-N-MC	brain:	n/a	n/a
29	FOXP2	chr3:89156498-89157033	SK-N-MC	brain:	n/a	chr3:89156503-89156515
30	REST	chr3:89156177-89157548	H1-neurons	neurons:	n/a	chr3:89156653-89156666 chr3:89156559-89156577 chr3:89156558-89156578 chr3:89156558-89156572 chr3:89156560-89156570
31	KAP1	chr3:89156485-89157491	U2OS	brain:	n/a	n/a
32	MXI1	chr3:89156337-89157071	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:89156482-89157628	H1-neurons	neurons:	n/a	n/a
34	TEAD4	chr3:89156474-89156941	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr3:89156501-89157041	H1-hESC	embryonic stem cell:	n/a	chr3:89156641-89156654 chr3:89156879-89156889 chr3:89156877-89156889
36	POLR2A	chr3:89156317-89157307	PFSK-1	brain:	n/a	n/a
37	KAP1	chr3:89156384-89157646	HEK293	kidney:	n/a	n/a
38	MAX	chr3:89156487-89157253	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr3:89156442-89157077	H1-neurons	neurons:	n/a	n/a
40	PAX5	chr3:89156355-89157004	GM12878	blood:	n/a	chr3:89156421-89156430 chr3:89156418-89156427 chr3:89156675-89156694
41	MAX	chr3:89156516-89156893	A549	lung:	n/a	n/a
42	ELF1	chr3:89156500-89156976	GM12878	blood:	n/a	n/a
43	PAX5	chr3:89156452-89156870	GM12878	blood:	n/a	chr3:89156675-89156694
44	MAX	chr3:89156468-89157368	ECC-1	luminal epithelium:	n/a	chr3:89157335-89157345
45	POLR2A	chr3:89156380-89157247	H1-neurons	neurons:	n/a	n/a
46	TCF3	chr3:89156486-89156893	GM12878	blood:	n/a	n/a
47	CEBPB	chr3:89156348-89156954	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:89156478-89156528	Hela-S3	cervix:	n/a
2	chr3:89156478-89156528	GM19239	blood:	n/a
3	chr3:89156478-89156528	ovcar-3	ovarian:	n/a
4	chr3:89156478-89156528	NT2-D1	testis:	n/a
5	chr3:89156478-89156528	GM06990	blood:	n/a
6	chr3:89156478-89156528	K562	blood:	n/a
7	chr3:89156478-89156528	HMEC	breast:	n/a
8	chr3:89156478-89156528	HUVEC	blood vessel:	n/a
9	chr3:89156478-89156528	T-47D	breast:	n/a
10	chr3:89156478-89156528	SK-N-SH_RA	brain:	n/a
11	chr3:89156478-89156528	HRCEpiC	kidney:	n/a
12	chr3:89156478-89156528	HCM	heart:	n/a
13	chr3:89156478-89156528	SAEC	small airway:	n/a
14	chr3:89156478-89156528	NH-A	brain:	n/a
15	chr3:89156478-89156528	AG10803	skin:	n/a
16	chr3:89156478-89156528	LNCaP	prostate:	n/a
17	chr3:89156478-89156528	GM12878	blood:	n/a
18	chr3:89156478-89156528	MCF10A-Er-Src	breast:	n/a
19	chr3:89156478-89156528	A549	lung:	n/a
20	chr3:89156478-89156528	CMK	blood:	n/a
21	chr3:89156478-89156528	ECC-1	luminal epithelium:	n/a
22	chr3:89156478-89156528	AoSMC	blood vessel:	n/a
23	chr3:89156478-89156528	Jurkat	blood:	n/a
24	chr3:89156478-89156528	GM12891	blood:	n/a
25	chr3:89156478-89156528	MCF-7	breast:	n/a
26	chr3:89156478-89156528	GM12892	blood:	n/a
27	chr3:89156478-89156528	HEEpiC	esophagus:	n/a
28	chr3:89156478-89156528	AG09319	gingival:	n/a
29	chr3:89156478-89156528	PFSK-1	brain:	n/a
30	chr3:89156478-89156528	HL-60	blood:	n/a
31	chr3:89156478-89156528	HCF	heart:	n/a
32	chr3:89156478-89156528	ProgFib	skin:	n/a
33	chr3:89156478-89156528	HCPEpiC	choroid plexus:	n/a
34	chr3:89156478-89156528	SK-N-SH	brain:	n/a
35	chr3:89156478-89156528	Hepatocyte	liver:	n/a
36	chr3:89156478-89156528	Caco-2	colon:	n/a
37	chr3:89156478-89156528	HAEpiC	amniotic membrane:	n/a
38	chr3:89156478-89156528	AG04449	skin:	fetal
39	chr3:89156478-89156528	HNPCEpiC	eye:	n/a
40	chr3:89156478-89156528	NHBE	bronchial:	n/a
41	chr3:89156478-89156528	IMR90	lung:	fetal
42	chr3:89156478-89156528	BJ	skin:	n/a
43	chr3:89156478-89156528	HCT-116	colon:	n/a
44	chr3:89156478-89156528	HIPEpiC	eye:	n/a
45	chr3:89156478-89156528	SK-N-MC	brain:	n/a
46	chr3:89156478-89156528	U87	brain:	n/a
47	chr3:89156478-89156528	AG09309	skin:	n/a
48	chr3:89156478-89156528	BE2_C	brain:	n/a
49	chr3:89156478-89156528	PANC-1	pancreas:	n/a
50	chr3:89156478-89156528	PrEC	prostate:	n/a

Variant related genes	Relation type
EPHA3	TF binding region
EPHA3	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11914680	1.00[CEU][hapmap]
rs11914760	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11916891	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs11918311	1.00[CEU][hapmap]
rs11919574	1.00[CEU][hapmap]
rs11921042	1.00[CEU][hapmap]
rs11928901	0.92[EUR][1000 genomes]
rs12486049	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs12487141	0.90[EUR][1000 genomes]
rs12490373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490659	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12491480	0.92[EUR][1000 genomes]
rs12493524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493527	0.92[EUR][1000 genomes]
rs12494615	1.00[CEU][hapmap]
rs12495783	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs12496609	0.92[EUR][1000 genomes]
rs13058761	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13058886	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13060198	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13075931	1.00[CEU][hapmap]
rs13084503	0.92[EUR][1000 genomes]
rs13089469	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13095092	0.82[EUR][1000 genomes]
rs13097212	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13097548	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13098003	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs13101118	1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap]
rs1512909	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs34493897	0.83[EUR][1000 genomes]
rs34638812	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34893903	0.92[EUR][1000 genomes]
rs34992749	0.92[EUR][1000 genomes]
rs35053334	0.92[EUR][1000 genomes]
rs35445148	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs4132274	1.00[CEU][hapmap]
rs56408441	0.83[EUR][1000 genomes]
rs56938121	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59668913	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71322851	0.92[EUR][1000 genomes]
rs71322854	0.92[EUR][1000 genomes]
rs71322855	0.92[EUR][1000 genomes]
rs71322856	0.92[EUR][1000 genomes]
rs71322857	0.82[EUR][1000 genomes]
rs71322858	0.83[EUR][1000 genomes]
rs7430987	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7432443	1.00[CEU][hapmap]
rs7631932	0.93[CEU][hapmap]
rs7635321	0.87[CEU][hapmap]
rs7637578	1.00[CEU][hapmap]
rs7638207	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7642606	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89152800-89156600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:89154400-89156600	Weak transcription	GM12878-XiMat	blood
3	chr3:89156000-89156600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:89156000-89156800	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:89156000-89157200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:89156000-89158200	Active TSS	Right Atrium	heart
7	chr3:89156000-89158800	Active TSS	Brain Germinal Matrix	brain
8	chr3:89156000-89159600	Active TSS	Fetal Brain Male	brain
9	chr3:89156000-89159800	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:89156200-89156600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr3:89156200-89156600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr3:89156200-89156600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr3:89156200-89156600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:89156200-89156600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:89156200-89156600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr3:89156200-89156600	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr3:89156200-89156600	Active TSS	Fetal Muscle Trunk	muscle
18	chr3:89156200-89156600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:89156200-89156800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
20	chr3:89156200-89156800	Active TSS	Colon Smooth Muscle	Colon
21	chr3:89156200-89156800	Bivalent/Poised TSS	Fetal Lung	lung
22	chr3:89156200-89157000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:89156200-89157000	Active TSS	Fetal Brain Female	brain
24	chr3:89156200-89157000	Active TSS	NH-A	brain
25	chr3:89156200-89157200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:89156200-89157200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr3:89156200-89157200	Active TSS	Brain Hippocampus Middle	brain
28	chr3:89156200-89157200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
29	chr3:89156200-89157400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:89156200-89157400	Flanking Active TSS	Osteobl	bone
31	chr3:89156200-89157600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr3:89156200-89157600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:89156200-89158200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:89156200-89158600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:89156200-89159200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:89156400-89156600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:89156400-89156600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:89156400-89156600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:89156400-89156600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:89156400-89156600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:89156400-89156600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:89156400-89156600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr3:89156400-89156600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:89156400-89156600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:89156400-89156600	Bivalent Enhancer	Liver	Liver
46	chr3:89156400-89156600	Active TSS	Esophagus	oesophagus
47	chr3:89156400-89156600	Active TSS	Fetal Muscle Leg	muscle
48	chr3:89156400-89156600	Flanking Active TSS	Fetal Stomach	stomach
49	chr3:89156400-89156600	Enhancers	Gastric	stomach
50	chr3:89156400-89156600	Enhancers	Pancreas	Pancrea

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