Variant report

Variant	rs73839167
Chromosome Location	chr3:52742725-52742726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
2	chr3:52738473..52741784-chr3:52742214..52745484,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163939	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000252787	Chromatin interaction
ENSG00000212493	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17052329	0.90[AFR][1000 genomes]
rs17052401	1.00[AMR][1000 genomes]
rs55662247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55971019	0.84[AFR][1000 genomes]
rs59277755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6803509	1.00[AMR][1000 genomes]
rs73839121	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839179	1.00[AMR][1000 genomes]
rs73839182	1.00[AMR][1000 genomes]
rs73839183	1.00[AMR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741000-52746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:52741000-52748200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52741000-52748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52741000-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52741000-52748800	Weak transcription	Lung	lung
6	chr3:52741200-52748200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52741400-52746600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52741400-52747000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
10	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52741600-52742800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:52741600-52743000	Strong transcription	NHDF-Ad	bronchial
13	chr3:52741600-52743600	Weak transcription	Left Ventricle	heart
14	chr3:52741600-52746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:52741600-52746400	Weak transcription	Gastric	stomach
16	chr3:52741600-52746400	Weak transcription	Spleen	Spleen
17	chr3:52741600-52746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:52741600-52747000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52741600-52747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:52741600-52748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:52741600-52748200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52741600-52748200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:52741600-52748400	Weak transcription	Colonic Mucosa	Colon
24	chr3:52741600-52748400	Weak transcription	Right Ventricle	heart
25	chr3:52741600-52748600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:52741600-52748600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:52741600-52752600	Weak transcription	Ovary	ovary
28	chr3:52741600-52752600	Weak transcription	A549	lung
29	chr3:52741600-52764000	Weak transcription	Small Intestine	intestine
30	chr3:52741600-52765600	Weak transcription	Esophagus	oesophagus
31	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
32	chr3:52741800-52742800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:52741800-52742800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:52741800-52743000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:52741800-52743000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:52741800-52743000	Strong transcription	HSMM	muscle
37	chr3:52741800-52743200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:52741800-52743200	Genic enhancers	HepG2	liver
39	chr3:52741800-52743400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:52741800-52743400	Strong transcription	Brain Substantia Nigra	brain
41	chr3:52741800-52743600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr3:52741800-52743600	Strong transcription	Placenta	Placenta
43	chr3:52741800-52744000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:52741800-52744000	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:52741800-52744600	Strong transcription	Fetal Intestine Large	intestine
46	chr3:52741800-52746800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:52741800-52747400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:52741800-52748400	Weak transcription	Fetal Heart	heart
49	chr3:52742000-52743000	Strong transcription	NH-A	brain
50	chr3:52742000-52743200	Strong transcription	Brain Anterior Caudate	brain

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