Variant report

Variant	rs3762580
Chromosome Location	chr2:11750374-11750375
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	POLR2A	chr2:11747782-11754276	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11742961..11746645-chr2:11747692..11751157,4	MCF-7	breast:
2	chr2:11678223..11684922-chr2:11747400..11752385,8	MCF-7	breast:
3	chr2:11620780..11623645-chr2:11748441..11751021,2	MCF-7	breast:

Variant related genes	Relation type
GREB1	TF binding region
ENSG00000264010	Chromatin interaction
ENSG00000196208	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11888586	0.86[ASN][1000 genomes]
rs12612679	0.86[ASN][1000 genomes]
rs12616734	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620008	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623029	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828298	0.93[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs56856746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60221670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61593826	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73175250	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:11733400-11750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:11733600-11750600	Weak transcription	Pancreas	Pancrea
13	chr2:11733600-11784000	Strong transcription	HepG2	liver
14	chr2:11736200-11765000	Weak transcription	Fetal Lung	lung
15	chr2:11736400-11755400	Weak transcription	Brain Substantia Nigra	brain
16	chr2:11736600-11750600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:11736800-11762800	Weak transcription	Fetal Heart	heart
18	chr2:11739200-11751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:11739200-11752000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:11739600-11750800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:11741400-11755400	Weak transcription	Liver	Liver
22	chr2:11741600-11750800	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:11742000-11750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:11742800-11751000	Strong transcription	Ovary	ovary
25	chr2:11743200-11765200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:11743400-11752600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:11743400-11765000	Weak transcription	Left Ventricle	heart
28	chr2:11744000-11753000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:11744800-11750400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:11745200-11765000	Weak transcription	Fetal Kidney	kidney
31	chr2:11747200-11767200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:11748000-11750800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:11748000-11766800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:11748400-11754200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:11748600-11767600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:11749000-11763200	Strong transcription	Fetal Stomach	stomach
37	chr2:11749000-11766800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:11749400-11751200	Strong transcription	Brain Angular Gyrus	brain
39	chr2:11749400-11763400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:11749600-11750800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:11749600-11751000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr2:11749600-11751600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:11749600-11752000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr2:11749600-11754000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:11749600-11754000	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:11749600-11759600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr2:11749800-11751200	Strong transcription	Brain Anterior Caudate	brain
48	chr2:11750000-11752800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:11750000-11760200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:11750200-11750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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