Variant report

Variant	rs6040562
Chromosome Location	chr20:11332155-11332156
allele	G/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: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs6040553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6040580	0.91[AFR][1000 genomes]
rs6040590	0.92[AFR][1000 genomes]
rs6040595	0.94[AFR][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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11330400-11332400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr20:11330400-11332600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr20:11330600-11332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:11330600-11332400	Enhancers	HMEC	breast
5	chr20:11330600-11333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:11330600-11334400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr20:11330800-11332400	Enhancers	Brain Substantia Nigra	brain
8	chr20:11330800-11333200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr20:11330800-11333600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:11330800-11334200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:11330800-11336200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:11331000-11332400	Enhancers	Psoas Muscle	Psoas
13	chr20:11331000-11333000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:11331000-11338400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr20:11331200-11332200	Enhancers	Brain Hippocampus Middle	brain
16	chr20:11331200-11332400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr20:11331200-11332800	Enhancers	Fetal Intestine Small	intestine
18	chr20:11331200-11333200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr20:11331200-11333800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr20:11331400-11332200	Enhancers	NHEK	skin
21	chr20:11331400-11333400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:11331600-11333000	Weak transcription	Fetal Lung	lung
23	chr20:11331800-11332200	Active TSS	Brain Germinal Matrix	brain
24	chr20:11331800-11332200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr20:11331800-11332200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr20:11331800-11333200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr20:11331800-11333400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr20:11332000-11332200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:11332000-11332400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:11332000-11332400	Enhancers	Brain Anterior Caudate	brain
31	chr20:11332000-11333200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr20:11332000-11333200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr20:11332000-11333400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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