Variant report

Variant	rs2799339
Chromosome Location	chr13:53644658-53644659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1343600	0.96[ASN][1000 genomes]
rs1343606	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1891942	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2799338	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799340	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799348	0.80[ASN][1000 genomes]
rs2806935	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2806938	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2806948	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2806961	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2806962	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2806967	0.87[ASN][1000 genomes]
rs2807004	0.80[ASN][1000 genomes]
rs4884340	0.96[ASN][1000 genomes]
rs4886137	0.85[ASN][1000 genomes]
rs7319933	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7322978	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323451	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7327235	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7986263	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9527056	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9563131	0.87[EUR][1000 genomes]
rs9568800	0.83[ASN][1000 genomes]
rs9568802	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568803	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53639200-53654800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr13:53643000-53648200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr13:53643200-53647400	Weak transcription	Brain Anterior Caudate	brain
4	chr13:53643200-53648800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:53643400-53647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:53643600-53645400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr13:53643600-53647200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:53643600-53648000	Weak transcription	Brain Germinal Matrix	brain
9	chr13:53643600-53649600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:53643800-53647200	Weak transcription	Brain Angular Gyrus	brain
11	chr13:53643800-53647200	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:53643800-53647200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr13:53643800-53647400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:53643800-53647400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:53643800-53647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:53643800-53649800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:53644000-53647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:53644000-53647200	Weak transcription	Brain Substantia Nigra	brain
19	chr13:53644000-53649200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:53644400-53647200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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