Variant report

Variant	rs9920007
Chromosome Location	chr15:56121060-56121061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55878826..55881608-chr15:56118579..56121069,2	MCF-7	breast:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	NEDD4	hsa-miR-30c-5p	chr15:56121051-56121073

Variant related genes	Relation type
ENSG00000171016	Chromatin interaction
NEDD4	miRNA target site

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10851598	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071229	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11853453	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906680	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912488	0.83[EUR][1000 genomes]
rs12912732	0.83[EUR][1000 genomes]
rs17819276	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28444575	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28448752	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3759865	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7180060	0.83[AMR][1000 genomes]
rs9788664	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9888655	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9888676	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[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:73 , 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	chr15:56112200-56121800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:56112400-56124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:56112600-56122000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:56112600-56122000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:56112600-56122200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:56112600-56123800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:56112600-56133600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:56114600-56128200	Weak transcription	Esophagus	oesophagus
11	chr15:56115400-56122400	Weak transcription	Aorta	Aorta
12	chr15:56115400-56148000	Weak transcription	Ovary	ovary
13	chr15:56115600-56121800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:56115800-56129800	Weak transcription	Hela-S3	cervix
15	chr15:56116200-56121800	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:56116400-56121800	Weak transcription	HSMMtube	muscle
17	chr15:56116400-56122200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:56116400-56122200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:56116400-56122400	Weak transcription	Fetal Intestine Small	intestine
20	chr15:56116400-56124800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:56116400-56129000	Weak transcription	NHLF	lung
22	chr15:56116400-56129600	Weak transcription	NHDF-Ad	bronchial
23	chr15:56116400-56133400	Weak transcription	Fetal Lung	lung
24	chr15:56116600-56122200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:56116600-56122200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:56116600-56122400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:56116600-56123800	Weak transcription	Adipose Nuclei	Adipose
28	chr15:56116600-56150600	Weak transcription	Right Ventricle	heart
29	chr15:56116800-56122200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
31	chr15:56117200-56122000	Weak transcription	Fetal Intestine Large	intestine
32	chr15:56117200-56122400	Weak transcription	Fetal Stomach	stomach
33	chr15:56117600-56131200	Weak transcription	Small Intestine	intestine
34	chr15:56118000-56121600	Weak transcription	Dnd41	blood
35	chr15:56118000-56121800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:56118000-56125800	Strong transcription	HSMM	muscle
37	chr15:56118600-56122400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:56118600-56151000	Weak transcription	Fetal Kidney	kidney
39	chr15:56118800-56122200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:56118800-56122200	Weak transcription	Left Ventricle	heart
41	chr15:56118800-56147000	Weak transcription	Gastric	stomach
42	chr15:56118800-56149200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:56118800-56151400	Weak transcription	Brain Anterior Caudate	brain
44	chr15:56119000-56121800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:56119200-56133000	Weak transcription	Primary T cells from cord blood	blood
46	chr15:56119400-56122600	Strong transcription	A549	lung
47	chr15:56119400-56123000	Enhancers	HMEC	breast
48	chr15:56119400-56124800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:56119400-56134800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:56119600-56121800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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