Variant report

Variant	rs3753661
Chromosome Location	chr1:226014342-226014343
allele	G/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	FOS	chr1:226014112-226014510	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:226014199-226014407	MCF10A-Er-Src	breast:	n/a	n/a
3	USF1	chr1:226014110-226014368	HepG2	liver:	n/a	chr1:226014220-226014231
4	MYC	chr1:226014043-226014510	MCF10A-Er-Src	breast:	n/a	chr1:226014220-226014231
5	FOS	chr1:226014167-226014402	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr1:226014252-226014411	K562	blood:	n/a	n/a
7	RFX5	chr1:226014231-226014350	HepG2	liver:	n/a	n/a
8	CEBPB	chr1:226014167-226014477	HepG2	liver:	n/a	n/a
9	MAX	chr1:226013986-226014593	HepG2	liver:	n/a	chr1:226014220-226014231
10	STAT3	chr1:226014108-226014510	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr1:226014245-226014347	HepG2	liver:	n/a	n/a
12	MAX	chr1:226014085-226014355	HepG2	liver:	n/a	chr1:226014220-226014231
13	CTCF	chr1:226014200-226014350	SAEC	small airway:	n/a	n/a
14	MXI1	chr1:226014146-226014415	HepG2	liver:	n/a	chr1:226014222-226014231
15	EP300	chr1:226014239-226014430	HepG2	liver:	n/a	n/a
16	SMC3	chr1:226014264-226014379	HepG2	liver:	n/a	n/a
17	FOXA2	chr1:226014142-226014384	HepG2	liver:	n/a	n/a
18	CEBPB	chr1:226014257-226014415	HepG2	liver:	n/a	n/a
19	STAT3	chr1:226014215-226014488	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr1:226014142-226014507	HepG2	liver:	n/a	n/a
21	MYC	chr1:226014042-226014534	MCF10A-Er-Src	breast:	n/a	chr1:226014220-226014231
22	MAX	chr1:226014019-226014618	HepG2	liver:	n/a	chr1:226014220-226014231
23	FOXA1	chr1:226014006-226014439	HepG2	liver:	n/a	n/a
24	STAT3	chr1:226014169-226014401	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr1:226014101-226014454	MCF10A-Er-Src	breast:	n/a	n/a
26	STAT3	chr1:226014117-226014475	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr1:226014137-226014410	MCF10A-Er-Src	breast:	n/a	n/a
28	CEBPB	chr1:226014173-226014517	MCF-7	breast:	n/a	n/a
29	CEBPB	chr1:226014274-226014389	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225992085..225994324-chr1:226013953..226015752,2	K562	blood:
2	chr1:225998339..226001333-chr1:226013491..226015022,2	K562	blood:

Variant related genes	Relation type
EPHX1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1011382	0.84[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs10753410	0.82[JPT][hapmap];0.93[MEX][hapmap]
rs10799326	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs12038486	0.84[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs12723313	0.80[ASN][1000 genomes]
rs12732891	1.00[YRI][hapmap]
rs12753757	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2078341	1.00[YRI][hapmap]
rs34878232	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738040	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3738043	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738047	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41467050	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4653678	1.00[YRI][hapmap]

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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
2	chr1:226000400-226015800	Enhancers	Ovary	ovary
3	chr1:226001800-226019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:226005600-226019400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:226005800-226019200	Weak transcription	NHLF	lung
6	chr1:226005800-226019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:226005800-226019400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:226006200-226016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:226006200-226019400	Weak transcription	HSMM	muscle
10	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
11	chr1:226006400-226014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:226006400-226016800	Weak transcription	Colonic Mucosa	Colon
13	chr1:226006400-226018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:226006400-226019400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:226006400-226019600	Weak transcription	Hela-S3	cervix
16	chr1:226006600-226016600	Weak transcription	Aorta	Aorta
17	chr1:226008800-226019400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:226009800-226015400	Enhancers	Colon Smooth Muscle	Colon
19	chr1:226010400-226015000	Enhancers	Gastric	stomach
20	chr1:226010800-226015400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:226010800-226016600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:226010800-226019200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:226011000-226014600	Enhancers	Right Atrium	heart
24	chr1:226011000-226015200	Enhancers	Brain Hippocampus Middle	brain
25	chr1:226011000-226015800	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:226011000-226015800	Genic enhancers	Fetal Muscle Leg	muscle
27	chr1:226011000-226016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:226011200-226014400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:226011200-226015000	Enhancers	Right Ventricle	heart
30	chr1:226011200-226015600	Enhancers	K562	blood
31	chr1:226011200-226016600	Enhancers	Pancreas	Pancrea
32	chr1:226011600-226015000	Enhancers	Stomach Mucosa	stomach
33	chr1:226011600-226015200	Genic enhancers	Fetal Intestine Small	intestine
34	chr1:226011800-226015000	Enhancers	Lung	lung
35	chr1:226011800-226016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:226012000-226014600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:226012000-226014800	Enhancers	Psoas Muscle	Psoas
38	chr1:226012000-226015400	Enhancers	Fetal Intestine Large	intestine
39	chr1:226012200-226015400	Enhancers	Spleen	Spleen
40	chr1:226012400-226015000	Enhancers	Placenta	Placenta
41	chr1:226012600-226015000	Strong transcription	Fetal Stomach	stomach
42	chr1:226012600-226016400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:226012600-226016600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:226012600-226016800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:226012600-226018000	Weak transcription	Fetal Brain Male	brain
46	chr1:226012800-226015000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:226012800-226015000	Enhancers	Left Ventricle	heart
48	chr1:226013000-226014400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:226013000-226014600	Enhancers	Esophagus	oesophagus
50	chr1:226013000-226014600	Enhancers	Skeletal Muscle Male	skeletal muscle

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