Variant report

Variant	rs62046606
Chromosome Location	chr15:56123628-56123629
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	chr15:56123505..56124315-chr2:199288626..199289422,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11550869	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238482	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17238489	0.94[EUR][1000 genomes]
rs17819282	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34555597	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55782406	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62043760	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62043761	0.95[EUR][1000 genomes]
rs62043763	0.96[EUR][1000 genomes]
rs62043764	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62043792	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62043793	0.92[EUR][1000 genomes]
rs62043796	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62043801	0.85[EUR][1000 genomes]
rs62043802	0.88[EUR][1000 genomes]
rs62043810	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62043815	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62043816	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62046605	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046641	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046642	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046643	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046648	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62046649	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62046650	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56095800-56128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56106000-56131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56112400-56124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:56112600-56123800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:56112600-56133600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:56114600-56128200	Weak transcription	Esophagus	oesophagus
7	chr15:56115400-56148000	Weak transcription	Ovary	ovary
8	chr15:56115800-56129800	Weak transcription	Hela-S3	cervix
9	chr15:56116400-56124800	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:56116400-56129000	Weak transcription	NHLF	lung
11	chr15:56116400-56129600	Weak transcription	NHDF-Ad	bronchial
12	chr15:56116400-56133400	Weak transcription	Fetal Lung	lung
13	chr15:56116600-56123800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:56116600-56150600	Weak transcription	Right Ventricle	heart
15	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
16	chr15:56117600-56131200	Weak transcription	Small Intestine	intestine
17	chr15:56118000-56125800	Strong transcription	HSMM	muscle
18	chr15:56118600-56151000	Weak transcription	Fetal Kidney	kidney
19	chr15:56118800-56147000	Weak transcription	Gastric	stomach
20	chr15:56118800-56149200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:56118800-56151400	Weak transcription	Brain Anterior Caudate	brain
22	chr15:56119200-56133000	Weak transcription	Primary T cells from cord blood	blood
23	chr15:56119400-56124800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:56119400-56134800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:56120000-56125600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr15:56120000-56126200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:56120000-56136800	Strong transcription	Liver	Liver
28	chr15:56120000-56144800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:56120000-56147800	Weak transcription	HepG2	liver
30	chr15:56120200-56125600	Strong transcription	NH-A	brain
31	chr15:56120200-56125800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:56120200-56126400	Strong transcription	Osteobl	bone
33	chr15:56120600-56127600	Weak transcription	Lung	lung
34	chr15:56120600-56146600	Weak transcription	Pancreas	Pancrea
35	chr15:56120800-56126600	Weak transcription	Psoas Muscle	Psoas
36	chr15:56120800-56147200	Weak transcription	Thymus	Thymus
37	chr15:56121200-56147200	Weak transcription	Spleen	Spleen
38	chr15:56121600-56126400	Strong transcription	Placenta	Placenta
39	chr15:56121800-56125000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:56121800-56125200	Strong transcription	Fetal Muscle Leg	muscle
41	chr15:56121800-56126200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:56121800-56126200	Strong transcription	HSMMtube	muscle
43	chr15:56121800-56135600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:56122000-56124200	Strong transcription	HUVEC	blood vessel
45	chr15:56122000-56125000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:56122000-56125200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:56122000-56136600	Strong transcription	Fetal Intestine Large	intestine
48	chr15:56122200-56124000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr15:56122200-56125000	Strong transcription	Left Ventricle	heart
50	chr15:56122200-56125200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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