Variant report

Variant	rs299823
Chromosome Location	chr17:63140960-63140961
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	chr17:63133396..63138666-chr17:63139121..63145017,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108370	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1010271	0.86[MEX][hapmap]
rs2007246	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2585862	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2869574	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299822	0.81[EUR][1000 genomes]
rs299824	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs34695575	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs387208	0.93[CEU][hapmap];0.92[CHB][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392449	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs419526	0.80[EUR][1000 genomes]
rs4427842	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs451403	0.80[EUR][1000 genomes]
rs7359499	1.00[CHB][hapmap];0.93[CHD][hapmap]

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	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv1009898	chr17:63135734-63146723	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs299823	C17orf60	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63134400-63143000	Weak transcription	Spleen	Spleen
2	chr17:63134400-63143200	Weak transcription	Esophagus	oesophagus
3	chr17:63134400-63169000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:63135800-63146800	Weak transcription	Thymus	Thymus
5	chr17:63136000-63142800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:63138600-63151200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:63139400-63143000	Weak transcription	GM12878-XiMat	blood
8	chr17:63140000-63141000	Enhancers	Brain Cingulate Gyrus	brain
9	chr17:63140000-63141000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr17:63140000-63141200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:63140000-63141200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr17:63140200-63142200	Enhancers	Fetal Thymus	thymus
13	chr17:63140400-63141000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:63140400-63141000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:63140400-63141000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:63140400-63142800	Weak transcription	Brain Hippocampus Middle	brain
17	chr17:63140600-63141000	Enhancers	Brain Anterior Caudate	brain
18	chr17:63140600-63141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:63140800-63141000	Enhancers	Brain Substantia Nigra	brain
20	chr17:63140800-63141000	Enhancers	Fetal Kidney	kidney
21	chr17:63140800-63143000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr17:63140800-63143000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr17:63140800-63143000	Weak transcription	Lung	lung
24	chr17:63140800-63143000	Weak transcription	Ovary	ovary
25	chr17:63140800-63143200	Weak transcription	Brain Angular Gyrus	brain

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