Variant report

Variant	rs6104738
Chromosome Location	chr20:11332858-11332859
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	chr20:11330194..11333067-chr20:11363546..11365974,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11698064	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13038948	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13039061	0.98[ASN][1000 genomes]
rs13043539	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535071	0.94[ASN][1000 genomes]
rs1535072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17800232	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1997876	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1997877	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2327399	0.89[EUR][1000 genomes]
rs2327402	0.94[ASN][1000 genomes]
rs28479511	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033092	0.80[EUR][1000 genomes]
rs6033095	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040515	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6074279	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074281	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074283	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074287	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074294	0.90[ASN][1000 genomes]
rs6078118	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6078132	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6078136	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6078138	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs6078140	0.99[ASN][1000 genomes]
rs6078141	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6078143	0.93[EUR][1000 genomes]
rs6078144	0.93[ASN][1000 genomes]
rs6078147	0.95[ASN][1000 genomes]
rs6104739	0.99[EUR][1000 genomes]
rs6104745	0.92[ASN][1000 genomes]
rs6108906	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6108909	0.89[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs722568	0.82[ASN][1000 genomes]
rs988788	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 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	chr20:11330600-11333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr20:11330600-11334400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr20:11330800-11333200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:11330800-11333600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr20:11330800-11334200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:11330800-11336200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:11331000-11333000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:11331000-11338400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:11331200-11333200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr20:11331200-11333800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:11331400-11333400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:11331600-11333000	Weak transcription	Fetal Lung	lung
13	chr20:11331800-11333200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr20:11331800-11333400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr20:11332000-11333200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr20:11332000-11333200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr20:11332000-11333400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr20:11332200-11333000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:11332200-11333000	Enhancers	Brain Germinal Matrix	brain
20	chr20:11332200-11334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:11332400-11334200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:11332400-11334800	Weak transcription	HMEC	breast
23	chr20:11332400-11336200	Weak transcription	Psoas Muscle	Psoas
24	chr20:11332400-11337400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:11332600-11333800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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