Variant report

Variant	rs12489835
Chromosome Location	chr3:69591454-69591455
allele	A/C
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	E2F6	chr3:69590804-69592178	H1-hESC	embryonic stem cell:	n/a	chr3:69591777-69591786 chr3:69591095-69591103 chr3:69591096-69591103 chr3:69591974-69591983 chr3:69591491-69591501 chr3:69591773-69591782 chr3:69591494-69591504 chr3:69591768-69591778 chr3:69591790-69591800
2	CTBP2	chr3:69590949-69592080	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:69591435-69592080	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:69591270-69591843	MCF10A-Er-Src	breast:	n/a	n/a
5	USF1	chr3:69591363-69591627	H1-hESC	embryonic stem cell:	n/a	chr3:69591544-69591557 chr3:69591416-69591432
6	TBP	chr3:69591271-69592241	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:69590811-69591835	HL-60	blood:	n/a	n/a
8	POLR2A	chr3:69590844-69591961	HL-60	blood:	n/a	n/a
9	SPI1	chr3:69591424-69591744	HL-60	blood:	n/a	chr3:69591514-69591521 chr3:69591505-69591512 chr3:69591520-69591527
10	USF1	chr3:69591369-69591744	H1-hESC	embryonic stem cell:	n/a	chr3:69591638-69591654 chr3:69591544-69591557 chr3:69591416-69591432
11	SIN3A	chr3:69590985-69592284	H1-hESC	embryonic stem cell:	n/a	chr3:69591590-69591599
12	MAX	chr3:69590775-69592151	H1-hESC	embryonic stem cell:	n/a	chr3:69591628-69591638 chr3:69591778-69591788 chr3:69591545-69591556 chr3:69591772-69591782 chr3:69591042-69591049
13	TAF1	chr3:69591342-69592230	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr3:69591162-69592113	H1-neurons	neurons:	n/a	chr3:69591982-69591995 chr3:69591640-69591653
15	MAX	chr3:69590854-69592141	H1-hESC	embryonic stem cell:	n/a	chr3:69591628-69591638 chr3:69591778-69591788 chr3:69591545-69591556 chr3:69591772-69591782 chr3:69591042-69591049
16	NANOG	chr3:69591434-69591708	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr3:69590644-69592126	H1-hESC	embryonic stem cell:	n/a	chr3:69591777-69591786 chr3:69591095-69591103 chr3:69591096-69591103 chr3:69591974-69591983 chr3:69591491-69591501 chr3:69591773-69591782 chr3:69591494-69591504 chr3:69591768-69591778 chr3:69591790-69591800
18	SPI1	chr3:69590886-69591779	HL-60	blood:	n/a	chr3:69591514-69591521 chr3:69591505-69591512 chr3:69591520-69591527

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12629703	0.93[ASN][1000 genomes]
rs12633054	0.89[ASN][1000 genomes]
rs12633166	0.93[ASN][1000 genomes]
rs62250896	0.89[ASN][1000 genomes]
rs62252577	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62252578	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62252579	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3426797	chr3:69433086-69777229	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69589600-69592400	Active TSS	HMEC	breast
2	chr3:69589800-69592400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:69589800-69592400	Active TSS	Brain Anterior Caudate	brain
4	chr3:69589800-69592400	Active TSS	Brain Substantia Nigra	brain
5	chr3:69590000-69591600	Active TSS	Spleen	Spleen
6	chr3:69590000-69592200	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:69590000-69592200	Active TSS	Brain Hippocampus Middle	brain
8	chr3:69590000-69592400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:69590000-69592400	Active TSS	Brain Angular Gyrus	brain
10	chr3:69590000-69592600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:69590000-69592600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:69590000-69592600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
13	chr3:69590200-69591600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr3:69590200-69591600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr3:69590200-69591800	Active TSS	Fetal Brain Male	brain
16	chr3:69590200-69592000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr3:69590200-69592000	Active TSS	NHEK	skin
18	chr3:69590200-69592200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:69590200-69592400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr3:69590200-69592400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr3:69590200-69592400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:69590200-69592600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:69590400-69591800	Flanking Active TSS	Right Ventricle	heart
24	chr3:69590400-69592000	Active TSS	Fetal Lung	lung
25	chr3:69590400-69592000	Active TSS	Left Ventricle	heart
26	chr3:69590400-69592200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr3:69590400-69592200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:69590400-69592200	Active TSS	Ovary	ovary
29	chr3:69590400-69592400	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr3:69590400-69592400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:69590400-69592400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:69590600-69591600	Active TSS	Fetal Heart	heart
33	chr3:69590600-69591800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:69590600-69592200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:69590600-69592200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:69590600-69592200	Bivalent/Poised TSS	A549	lung
37	chr3:69590600-69592400	Active TSS	Right Atrium	heart
38	chr3:69590600-69592600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr3:69590800-69592000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:69590800-69592000	Bivalent/Poised TSS	Thymus	Thymus
41	chr3:69590800-69592200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:69590800-69592200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:69590800-69592200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:69590800-69592200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:69590800-69592200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr3:69590800-69592200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr3:69590800-69592200	Active TSS	Fetal Kidney	kidney
48	chr3:69590800-69592400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:69590800-69592400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:69590800-69592600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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