Variant report

Variant	rs56239979
Chromosome Location	chr3:142522753-142522754
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142442488..142444417-chr3:142520460..142522860,2	MCF-7	breast:
2	chr3:142294703..142296575-chr3:142522509..142525334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11717988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140436	0.82[AMR][1000 genomes]
rs55655603	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55851231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246347	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73230583	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230587	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73230588	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73230590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000631	chr3:142516367-142572058	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142468200-142525200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:142468400-142525200	Weak transcription	Fetal Brain Male	brain
3	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
4	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
5	chr3:142468600-142525200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:142490200-142529400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:142490400-142522800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:142495400-142527000	Weak transcription	Brain Angular Gyrus	brain
11	chr3:142498600-142522800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:142498600-142526800	Weak transcription	Osteobl	bone
13	chr3:142499000-142527000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:142499400-142547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:142501600-142525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:142501600-142525600	Weak transcription	Fetal Stomach	stomach
17	chr3:142501800-142527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:142501800-142528000	Weak transcription	Left Ventricle	heart
19	chr3:142501800-142535600	Weak transcription	Aorta	Aorta
20	chr3:142502000-142529400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:142502400-142522800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:142504200-142523200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:142510400-142527200	Weak transcription	A549	lung
24	chr3:142510600-142523600	Weak transcription	HepG2	liver
25	chr3:142513600-142523400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:142513600-142527200	Weak transcription	Brain Substantia Nigra	brain
27	chr3:142513800-142523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:142514600-142523400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:142514800-142572000	Weak transcription	Right Ventricle	heart
30	chr3:142515000-142523400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:142515000-142530800	Weak transcription	HSMM	muscle
32	chr3:142515600-142527000	Weak transcription	K562	blood
33	chr3:142517600-142526800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:142517800-142523200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:142518800-142527200	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:142519000-142572000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:142519200-142523400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:142519200-142526600	Weak transcription	NHLF	lung
39	chr3:142519800-142530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:142520800-142525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:142521000-142522800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:142521000-142523200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:142521200-142523200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:142521400-142523000	Strong transcription	Ovary	ovary
45	chr3:142521400-142525000	Strong transcription	Adipose Nuclei	Adipose
46	chr3:142521400-142525200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:142521400-142528800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:142521600-142523200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:142521600-142526800	Weak transcription	NH-A	brain
50	chr3:142522000-142522800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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