Variant report

Variant	rs12050658
Chromosome Location	chr15:73451781-73451782
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73414122..73416598-chr15:73451749..73454590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1116880	0.90[EUR][1000 genomes]
rs11634084	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12050685	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12050774	0.88[EUR][1000 genomes]
rs1479338	0.88[EUR][1000 genomes]
rs1479339	0.88[EUR][1000 genomes]
rs17762146	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17762516	0.85[EUR][1000 genomes]
rs17762600	0.88[EUR][1000 genomes]
rs17829830	0.88[EUR][1000 genomes]
rs17829957	0.87[EUR][1000 genomes]
rs1812835	0.87[EUR][1000 genomes]
rs1964543	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2415148	0.84[EUR][1000 genomes]
rs3985588	0.93[EUR][1000 genomes]
rs55646651	0.88[EUR][1000 genomes]
rs55868723	0.90[EUR][1000 genomes]
rs55939596	0.87[EUR][1000 genomes]
rs56215298	0.87[EUR][1000 genomes]
rs56348595	0.87[EUR][1000 genomes]
rs59066156	0.96[EUR][1000 genomes]
rs62015460	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62015484	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62015499	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62015500	0.83[EUR][1000 genomes]
rs62015502	0.82[EUR][1000 genomes]
rs62015504	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62016808	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62016813	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62016850	0.88[ASN][1000 genomes]
rs62016851	0.80[EUR][1000 genomes]
rs62016853	0.88[EUR][1000 genomes]
rs62016854	0.87[EUR][1000 genomes]
rs62016856	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016857	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016858	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62017774	0.87[EUR][1000 genomes]
rs62017776	0.87[EUR][1000 genomes]
rs7169083	0.85[EUR][1000 genomes]
rs74022925	0.87[EUR][1000 genomes]
rs74025262	0.88[EUR][1000 genomes]
rs7497992	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806496	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
3	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:73429000-73456600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:73430200-73466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:73431800-73453800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:73443600-73456600	Weak transcription	Fetal Kidney	kidney
8	chr15:73445600-73457400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:73447200-73470000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:73447600-73457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:73447600-73457800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:73447800-73458000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:73448000-73457000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:73448000-73469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:73448600-73455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:73448800-73454400	Weak transcription	Psoas Muscle	Psoas
17	chr15:73448800-73458000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:73448800-73458000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:73449000-73454400	Weak transcription	Aorta	Aorta
20	chr15:73449000-73458000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:73449200-73458000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:73449200-73458400	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:73449200-73469000	Weak transcription	Ovary	ovary
24	chr15:73449400-73466600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:73449600-73453000	Weak transcription	Gastric	stomach
26	chr15:73449800-73454600	Weak transcription	Lung	lung
27	chr15:73449800-73456600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:73449800-73457800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:73450000-73453000	Weak transcription	Left Ventricle	heart
30	chr15:73450000-73453800	Weak transcription	Fetal Lung	lung
31	chr15:73450000-73453800	Weak transcription	Fetal Stomach	stomach
32	chr15:73450000-73454400	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:73450000-73454600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:73450000-73454800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:73450000-73457400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:73450000-73457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:73450000-73457800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:73450000-73458000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:73450000-73475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:73450000-73477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:73451000-73457800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:73451400-73452200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:73451400-73456000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:73451400-73456400	Weak transcription	Fetal Intestine Small	intestine

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