Variant report

Variant	rs73883589
Chromosome Location	chr3:179371416-179371417
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	chr3:179370232-179372454	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:179370265-179371759	HL-60	blood:	n/a	n/a
3	HEY1	chr3:179370754-179371632	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:179370317-179371626	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr3:179370741-179371949	SK-N-SH	brain:	n/a	chr3:179370761-179370772 chr3:179371439-179371448
6	TAF1	chr3:179371022-179371539	Hela-S3	cervix:	n/a	n/a
7	NFIC	chr3:179370309-179371625	ECC-1	luminal epithelium:	n/a	n/a
8	YY1	chr3:179370902-179371536	SK-N-SH_RA	brain:	n/a	chr3:179371439-179371448
9	RAD21	chr3:179371032-179371550	H1-hESC	embryonic stem cell:	n/a	n/a
10	BRCA1	chr3:179371251-179371419	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:179370303-179371629	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:179370420-179371596	MCF-7	breast:	n/a	n/a
13	SIN3A	chr3:179370381-179371712	GM12878	blood:	n/a	chr3:179371520-179371531
14	POLR2A	chr3:179370328-179371691	NB4	blood:	n/a	n/a
15	MTA3	chr3:179370953-179371723	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:179370247-179371543	MCF-7	breast:	n/a	n/a
17	MAX	chr3:179370094-179372626	HCT-116	colon:	n/a	chr3:179372121-179372130
18	POLR2A	chr3:179370847-179371643	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:179370392-179371528	Hela-S3	cervix:	n/a	n/a
20	RUNX3	chr3:179370072-179371843	GM12878	blood:	n/a	n/a
21	CTCF	chr3:179370248-179371478	GM12878	blood:	n/a	n/a
22	RCOR1	chr3:179371132-179371739	Hela-S3	cervix:	n/a	n/a
23	TAF1	chr3:179371134-179371505	K562	blood:	n/a	n/a
24	POLR2A	chr3:179370304-179371660	GM18951	blood:	n/a	n/a
25	TAF1	chr3:179370461-179371472	HepG2	liver:	n/a	n/a
26	MAX	chr3:179370134-179371743	A549	lung:	n/a	n/a
27	USF1	chr3:179370993-179371419	SK-N-SH	brain:	n/a	chr3:179371226-179371235
28	SIN3AK20	chr3:179370276-179371736	SK-N-SH	brain:	n/a	n/a
29	YY1	chr3:179370529-179371425	GM12891	blood:	n/a	chr3:179370761-179370772
30	SIN3AK20	chr3:179370118-179371808	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:179370251-179372409	IMR90	lung:	n/a	n/a
32	TBP	chr3:179371197-179371507	GM12878	blood:	n/a	n/a
33	FOXA1	chr3:179371140-179371557	T-47D	breast:	n/a	n/a
34	MAX	chr3:179370541-179371529	HepG2	liver:	n/a	n/a
35	CTCF	chr3:179371300-179371450	HRE	kidney:	n/a	n/a
36	ZBTB7A	chr3:179370280-179371779	ECC-1	luminal epithelium:	n/a	chr3:179370729-179370738
37	UBTF	chr3:179370718-179371578	K562	blood:	n/a	n/a
38	TEAD4	chr3:179370139-179371544	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr3:179370170-179371655	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:179371017-179371784	GM12878	blood:	n/a	n/a
41	MXI1	chr3:179370934-179371648	Hela-S3	cervix:	n/a	n/a
42	MAX	chr3:179370140-179371704	SK-N-SH	brain:	n/a	n/a
43	CTCF	chr3:179371112-179371448	T-47D	breast:	n/a	n/a
44	FOXM1	chr3:179370883-179371758	GM12878	blood:	n/a	n/a
45	MXI1	chr3:179371135-179371444	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:179370400-179371509	ECC-1	luminal epithelium:	n/a	n/a
47	STAT5A	chr3:179370953-179371654	GM12878	blood:	n/a	n/a
48	YY1	chr3:179370621-179371419	HCT-116	colon:	n/a	chr3:179370761-179370772
49	BHLHE40	chr3:179370984-179371521	HepG2	liver:	n/a	chr3:179371226-179371235
50	MYC	chr3:179370979-179371423	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:172467247..172468788-chr3:179370430..179372469,2	MCF-7	breast:
2	chr3:179279377..179281917-chr3:179370859..179372461,2	K562	blood:
3	chr3:179279862..179282588-chr3:179370567..179372088,2	MCF-7	breast:

Variant related genes	Relation type
USP13	TF binding region
ENSG00000243977	TF binding region
ENSG00000114346	Chromatin interaction
ENSG00000136518	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12631991	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276803	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv3400340	chr3:179369683-179372231	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	esv3450815	chr3:179370008-179372006	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179369600-179372400	Active TSS	NHDF-Ad	bronchial
2	chr3:179369600-179372600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:179369800-179371800	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:179369800-179372000	Active TSS	Stomach Smooth Muscle	stomach
5	chr3:179369800-179372200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:179369800-179372200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:179369800-179372200	Active TSS	Fetal Brain Female	brain
8	chr3:179369800-179372400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:179369800-179372400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:179369800-179372400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:179369800-179372400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:179369800-179372400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:179369800-179372600	Active TSS	HSMMtube	muscle
14	chr3:179370000-179371600	Active TSS	Adipose Nuclei	Adipose
15	chr3:179370000-179371600	Active TSS	Fetal Muscle Trunk	muscle
16	chr3:179370000-179371800	Active TSS	Brain Substantia Nigra	brain
17	chr3:179370000-179371800	Active TSS	Gastric	stomach
18	chr3:179370000-179372000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:179370000-179372000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:179370000-179372000	Active TSS	Primary T cells from cord blood	blood
21	chr3:179370000-179372000	Active TSS	Brain Angular Gyrus	brain
22	chr3:179370000-179372000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:179370000-179372000	Active TSS	Fetal Lung	lung
24	chr3:179370000-179372000	Active TSS	Fetal Stomach	stomach
25	chr3:179370000-179372000	Active TSS	HMEC	breast
26	chr3:179370000-179372200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:179370000-179372200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr3:179370000-179372200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:179370000-179372200	Active TSS	Aorta	Aorta
30	chr3:179370000-179372200	Active TSS	Fetal Brain Male	brain
31	chr3:179370000-179372200	Active TSS	HSMM	muscle
32	chr3:179370000-179372600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:179370000-179372600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:179370000-179372600	Active TSS	Fetal Kidney	kidney
35	chr3:179370000-179372600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr3:179370000-179372800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:179370000-179372800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:179370000-179373000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr3:179370000-179373200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:179370200-179371600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:179370200-179371600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr3:179370200-179372000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:179370200-179372000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr3:179370200-179372000	Active TSS	Osteobl	bone
45	chr3:179370200-179372200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:179370200-179372200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:179370200-179372200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:179370200-179372200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr3:179370200-179372200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:179370200-179372200	Active TSS	Brain Anterior Caudate	brain

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