Variant report

Variant	rs6098006
Chromosome Location	chr20:53095830-53095831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53095783..53096550-chr20:53256431..53257396,3	MCF-7	breast:
2	chr20:53095482..53097034-chr20:53262598..53264162,9	MCF-7	breast:
3	chr20:53084969..53087855-chr20:53094880..53097639,2	MCF-7	breast:
4	chr20:53094793..53096626-chr20:53100134..53103148,3	MCF-7	breast:
5	chr20:53067433..53069648-chr20:53093856..53096720,2	MCF-7	breast:
6	chr20:53094603..53097316-chr20:53132108..53133984,2	MCF-7	breast:
7	chr20:53073105..53076272-chr20:53092801..53096708,6	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11907464	0.82[EUR][1000 genomes]
rs13040866	0.82[EUR][1000 genomes]
rs13042185	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13042986	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13044898	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1330017	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16999643	0.89[CEU][hapmap]
rs34310366	0.97[EUR][1000 genomes]
rs34433522	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34502501	0.97[EUR][1000 genomes]
rs34616206	0.98[EUR][1000 genomes]
rs34683517	0.97[EUR][1000 genomes]
rs35269605	0.87[EUR][1000 genomes]
rs35276316	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35321528	0.89[EUR][1000 genomes]
rs6014019	0.89[CEU][hapmap]
rs6014020	0.89[CEU][hapmap]
rs6014027	1.00[CEU][hapmap]
rs6014032	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6023244	0.88[CEU][hapmap]
rs6023245	0.88[CEU][hapmap]
rs6023251	0.88[CEU][hapmap]
rs6023254	0.89[CEU][hapmap]
rs6023269	0.82[EUR][1000 genomes]
rs6023270	0.82[EUR][1000 genomes]
rs6023272	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023273	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023274	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023275	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023276	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023291	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6023307	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6023309	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6091886	0.88[CEU][hapmap]
rs6091890	0.81[EUR][1000 genomes]
rs6091891	1.00[CEU][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098005	0.84[EUR][1000 genomes]
rs6098007	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098008	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098009	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098011	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs66631852	0.87[EUR][1000 genomes]
rs67687183	0.97[EUR][1000 genomes]
rs922398	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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	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
2	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53093400-53096200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:53093400-53096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:53093400-53106400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:53093600-53096400	Active TSS	Fetal Brain Female	brain
5	chr20:53093800-53099000	Weak transcription	Ovary	ovary
6	chr20:53094000-53111600	Weak transcription	Fetal Muscle Leg	muscle
7	chr20:53094200-53096200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:53094400-53096000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:53095000-53096000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:53095200-53096000	Weak transcription	Osteobl	bone
11	chr20:53095400-53096000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr20:53095400-53096400	Weak transcription	NHDF-Ad	bronchial
13	chr20:53095600-53096000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:53095600-53096600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr20:53095600-53096800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr20:53095600-53097200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr20:53095800-53096000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr20:53095800-53096000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:53095800-53096000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr20:53095800-53096000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:53095800-53096000	Bivalent Enhancer	Fetal Brain Male	brain
22	chr20:53095800-53096200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr20:53095800-53096600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr20:53095800-53096600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:53095800-53096800	Enhancers	HUES6 Cell Line	embryonic stem cell

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