Variant report

Variant	rs59039394
Chromosome Location	chr2:54806667-54806668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
2	chr2:54735530..54737587-chr2:54805600..54807327,2	MCF-7	breast:
3	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11888386	1.00[EUR][1000 genomes]
rs17046281	1.00[EUR][1000 genomes]
rs57381328	1.00[EUR][1000 genomes]
rs57623434	1.00[EUR][1000 genomes]
rs57749522	1.00[EUR][1000 genomes]
rs58833605	1.00[EUR][1000 genomes]
rs58920119	1.00[EUR][1000 genomes]
rs60282658	1.00[EUR][1000 genomes]
rs60410507	1.00[EUR][1000 genomes]
rs6705313	1.00[EUR][1000 genomes]
rs6714663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6740557	1.00[EUR][1000 genomes]
rs6751570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72906405	1.00[EUR][1000 genomes]
rs72906407	1.00[EUR][1000 genomes]
rs72906419	1.00[EUR][1000 genomes]
rs72906421	1.00[EUR][1000 genomes]
rs72906425	1.00[EUR][1000 genomes]
rs72906426	1.00[EUR][1000 genomes]
rs72911566	1.00[EUR][1000 genomes]
rs72911570	1.00[EUR][1000 genomes]
rs72911573	1.00[EUR][1000 genomes]
rs72913008	1.00[EUR][1000 genomes]
rs72913540	1.00[EUR][1000 genomes]
rs72913543	1.00[EUR][1000 genomes]
rs72913547	1.00[EUR][1000 genomes]
rs72913549	1.00[EUR][1000 genomes]
rs72913551	1.00[EUR][1000 genomes]
rs72915537	1.00[EUR][1000 genomes]
rs72915543	1.00[EUR][1000 genomes]
rs72915544	1.00[EUR][1000 genomes]
rs72915554	1.00[EUR][1000 genomes]
rs72915563	1.00[EUR][1000 genomes]
rs72918782	1.00[EUR][1000 genomes]
rs72918788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72920524	1.00[EUR][1000 genomes]
rs72920525	1.00[EUR][1000 genomes]
rs72920549	1.00[EUR][1000 genomes]
rs72920550	1.00[EUR][1000 genomes]
rs72920563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72920576	1.00[EUR][1000 genomes]
rs7572839	1.00[EUR][1000 genomes]
rs7580158	1.00[EUR][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
4	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
5	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:54796800-54806800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:54796800-54807400	Enhancers	Psoas Muscle	Psoas
8	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
10	chr2:54797400-54808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:54797800-54807000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:54800000-54807400	Enhancers	Right Ventricle	heart
13	chr2:54800800-54807000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54801600-54808600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:54801800-54807400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:54801800-54811000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:54802000-54807000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:54802000-54808400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:54802000-54816400	Enhancers	Liver	Liver
20	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
21	chr2:54802400-54808600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:54803000-54807200	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:54803000-54807200	Weak transcription	Dnd41	blood
24	chr2:54803000-54807800	Enhancers	Brain Hippocampus Middle	brain
25	chr2:54803200-54807000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:54803200-54807600	Enhancers	HMEC	breast
27	chr2:54803400-54807200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:54803600-54806800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:54803600-54807000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:54803600-54807200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:54803600-54807200	Enhancers	Brain Substantia Nigra	brain
32	chr2:54803600-54807400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:54803600-54808400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:54803800-54807200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:54803800-54807200	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:54803800-54807600	Enhancers	Colon Smooth Muscle	Colon
37	chr2:54804000-54807000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:54804000-54807400	Enhancers	Fetal Heart	heart
39	chr2:54804000-54808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:54804000-54809400	Enhancers	Fetal Kidney	kidney
41	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:54804200-54807800	Enhancers	Fetal Lung	lung
43	chr2:54804200-54808600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:54804200-54809400	Enhancers	Thymus	Thymus
45	chr2:54804400-54807200	Enhancers	Fetal Intestine Small	intestine
46	chr2:54804400-54807600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:54804400-54807800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54804400-54808000	Enhancers	Fetal Stomach	stomach
49	chr2:54804600-54809800	Enhancers	Fetal Intestine Large	intestine
50	chr2:54804600-54814600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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