Variant report

Variant	rs16999736
Chromosome Location	chr20:53142895-53142896
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53127125..53128837-chr20:53140416..53143219,2	MCF-7	breast:
2	chr20:53134328..53136096-chr20:53140905..53143136,2	MCF-7	breast:
3	chr20:53140576..53144414-chr20:53148249..53150515,4	MCF-7	breast:
4	chr20:53139463..53141004-chr20:53141568..53144031,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10485786	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16999731	1.00[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16999732	0.89[ASW][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16999764	0.86[CHD][hapmap]
rs2426521	0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs2426522	0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2426525	0.98[ASN][1000 genomes]
rs2426526	0.96[ASN][1000 genomes]
rs2426529	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs2426530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2426531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2426535	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2426536	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[ASN][1000 genomes]
rs57402636	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6014050	0.82[CHD][hapmap]
rs6023344	0.96[ASN][1000 genomes]
rs6091909	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6098044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6098064	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs6098074	0.86[CHD][hapmap]
rs726770	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs7272302	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7274532	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs73276924	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8126261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974461	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53120800-53148800	Weak transcription	Left Ventricle	heart
2	chr20:53129600-53149200	Weak transcription	Aorta	Aorta
3	chr20:53140400-53143000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr20:53140400-53143200	Enhancers	Fetal Brain Female	brain
5	chr20:53140400-53144000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr20:53140600-53143200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:53140600-53143600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr20:53140600-53143800	Enhancers	Fetal Brain Male	brain
9	chr20:53140800-53143000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:53140800-53144200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr20:53141400-53143000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:53141400-53143200	Enhancers	Fetal Lung	lung
13	chr20:53141400-53144200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr20:53141600-53143000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:53142000-53143600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr20:53142000-53143600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr20:53142000-53144200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr20:53142200-53143000	Enhancers	NHLF	lung
19	chr20:53142200-53143400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:53142200-53143800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:53142400-53143000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr20:53142400-53143000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:53142400-53143000	Enhancers	Adipose Nuclei	Adipose
24	chr20:53142400-53143200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:53142400-53143200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr20:53142400-53143200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:53142400-53143200	Enhancers	HUVEC	blood vessel
28	chr20:53142400-53143200	Enhancers	NH-A	brain
29	chr20:53142400-53143400	Enhancers	Osteobl	bone
30	chr20:53142400-53143800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:53142400-53144000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr20:53142600-53143000	Enhancers	Ovary	ovary
33	chr20:53142800-53143000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr20:53142800-53143000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr20:53142800-53143000	Enhancers	Brain Germinal Matrix	brain
36	chr20:53142800-53143000	Enhancers	Psoas Muscle	Psoas
37	chr20:53142800-53143200	Enhancers	H9 Cell Line	embryonic stem cell
38	chr20:53142800-53143200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr20:53142800-53143200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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