Variant report

Variant	rs12753757
Chromosome Location	chr1:226012076-226012077
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	chr1:226011974-226013818	A549	lung:	n/a	n/a
2	EGR1	chr1:226011530-226012126	K562	blood:	n/a	chr1:226011849-226011859 chr1:226011848-226011862 chr1:226011844-226011854 chr1:226011850-226011860 chr1:226011836-226011843 chr1:226011728-226011735 chr1:226011848-226011863 chr1:226011841-226011850 chr1:226011849-226011862 chr1:226011850-226011860 chr1:226011849-226011862 chr1:226011769-226011791 chr1:226011850-226011861 chr1:226011844-226011866 chr1:226011849-226011862 chr1:226011850-226011859 chr1:226011840-226011853

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226009795..226012080-chr1:226012833..226016826,4	MCF-7	breast:

Variant related genes	Relation type
EPHX1	TF binding region
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12723313	0.82[ASN][1000 genomes]
rs34878232	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738040	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738043	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738047	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3753661	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766934	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41467050	0.95[AMR][1000 genomes];0.84[EUR][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	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:91 , 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	chr1:226005800-226012400	Weak transcription	Placenta	Placenta
6	chr1:226005800-226013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:226005800-226013400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:226005800-226019200	Weak transcription	NHLF	lung
9	chr1:226005800-226019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:226005800-226019400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:226006200-226013200	Weak transcription	HSMMtube	muscle
12	chr1:226006200-226013600	Weak transcription	Small Intestine	intestine
13	chr1:226006200-226016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:226006200-226019400	Weak transcription	HSMM	muscle
15	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
16	chr1:226006400-226012600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:226006400-226013000	Weak transcription	Osteobl	bone
18	chr1:226006400-226014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:226006400-226014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:226006400-226016800	Weak transcription	Colonic Mucosa	Colon
21	chr1:226006400-226018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:226006400-226019400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:226006400-226019600	Weak transcription	Hela-S3	cervix
24	chr1:226006600-226016600	Weak transcription	Aorta	Aorta
25	chr1:226007800-226012200	Weak transcription	Spleen	Spleen
26	chr1:226008600-226013200	Weak transcription	Fetal Kidney	kidney
27	chr1:226008800-226012200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:226008800-226013400	Weak transcription	HMEC	breast
29	chr1:226008800-226019400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:226009400-226012600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:226009400-226013400	Genic enhancers	Fetal Lung	lung
32	chr1:226009800-226015400	Enhancers	Colon Smooth Muscle	Colon
33	chr1:226010000-226012800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:226010200-226012200	Genic enhancers	Stomach Smooth Muscle	stomach
35	chr1:226010200-226013600	Enhancers	Brain Substantia Nigra	brain
36	chr1:226010400-226015000	Enhancers	Gastric	stomach
37	chr1:226010800-226013000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:226010800-226013000	Weak transcription	Esophagus	oesophagus
39	chr1:226010800-226015400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:226010800-226016600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:226010800-226019200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:226011000-226012600	Enhancers	HepG2	liver
43	chr1:226011000-226013600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:226011000-226013800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr1:226011000-226014600	Enhancers	Right Atrium	heart
46	chr1:226011000-226015200	Enhancers	Brain Hippocampus Middle	brain
47	chr1:226011000-226015800	Enhancers	Fetal Muscle Trunk	muscle
48	chr1:226011000-226015800	Genic enhancers	Fetal Muscle Leg	muscle
49	chr1:226011000-226016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:226011200-226012600	Genic enhancers	Fetal Stomach	stomach

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