Variant report

Variant	rs72938239
Chromosome Location	chr3:111580418-111580419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111580329..111581908-chr3:111582056..111583865,2	MCF-7	breast:
2	chr3:111579110..111581393-chr3:111581603..111584247,2	MCF-7	breast:
3	chr14:77786295..77788288-chr3:111579023..111581381,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1282974	0.83[AMR][1000 genomes]
rs57784706	1.00[AMR][1000 genomes]
rs72936491	0.83[AMR][1000 genomes]
rs72938226	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938229	0.83[AMR][1000 genomes]
rs72938231	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938235	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938244	0.80[AFR][1000 genomes];1.00[AMR][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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:111577400-111581000	Active TSS	Right Ventricle	heart
2	chr3:111577400-111581200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:111577400-111582000	Active TSS	Aorta	Aorta
4	chr3:111577400-111582000	Active TSS	HSMMtube	muscle
5	chr3:111577600-111581200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:111577600-111581800	Active TSS	Left Ventricle	heart
7	chr3:111577800-111580600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:111577800-111580600	Active TSS	Lung	lung
9	chr3:111577800-111580800	Active TSS	NHDF-Ad	bronchial
10	chr3:111577800-111581000	Active TSS	Rectal Smooth Muscle	rectum
11	chr3:111578000-111580600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:111578000-111580800	Active TSS	NHLF	lung
13	chr3:111578000-111581000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:111578200-111580600	Active TSS	Fetal Muscle Trunk	muscle
15	chr3:111578400-111581600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:111578800-111580800	Active TSS	Brain Hippocampus Middle	brain
17	chr3:111579000-111580600	Active TSS	Psoas Muscle	Psoas
18	chr3:111579200-111580800	Flanking Active TSS	Liver	Liver
19	chr3:111579200-111581200	Active TSS	Colonic Mucosa	Colon
20	chr3:111579200-111581400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:111579400-111581000	Weak transcription	Spleen	Spleen
22	chr3:111579400-111585000	Weak transcription	Gastric	stomach
23	chr3:111579600-111580800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:111579600-111584800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:111579800-111580600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:111579800-111580600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr3:111579800-111580600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:111579800-111580600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:111579800-111580600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:111579800-111580600	Flanking Active TSS	Fetal Kidney	kidney
31	chr3:111579800-111580600	Bivalent Enhancer	Fetal Thymus	thymus
32	chr3:111579800-111580800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
33	chr3:111579800-111580800	Enhancers	Brain Germinal Matrix	brain
34	chr3:111579800-111581600	Transcr. at gene 5' and 3'	NHEK	skin
35	chr3:111579800-111582400	Weak transcription	Small Intestine	intestine
36	chr3:111579800-111584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:111579800-111588400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:111579800-111589000	Weak transcription	Pancreas	Pancrea
39	chr3:111580000-111580600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:111580000-111580600	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:111580000-111580600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:111580000-111580600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr3:111580000-111580600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:111580000-111580600	Flanking Active TSS	A549	lung
45	chr3:111580000-111580800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
46	chr3:111580000-111580800	Flanking Active TSS	HUVEC	blood vessel
47	chr3:111580000-111581000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:111580000-111581400	Flanking Active TSS	Hela-S3	cervix
49	chr3:111580000-111589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:111580200-111580600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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