Variant report

Variant	rs34708622
Chromosome Location	chr13:53643778-53643779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53542013..53542636-chr13:53643135..53643785,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10507575	0.83[EUR][1000 genomes]
rs12860364	0.81[EUR][1000 genomes]
rs12864008	0.85[ASN][1000 genomes]
rs12865218	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12866736	0.85[ASN][1000 genomes]
rs12867491	0.97[EUR][1000 genomes]
rs12868253	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12869523	0.97[EUR][1000 genomes]
rs12870777	0.97[EUR][1000 genomes]
rs12871248	0.97[EUR][1000 genomes]
rs12874939	0.97[EUR][1000 genomes]
rs12876105	0.97[EUR][1000 genomes]
rs12876387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12876786	0.94[EUR][1000 genomes]
rs12877178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12877599	0.97[EUR][1000 genomes]
rs12877758	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12877912	0.94[EUR][1000 genomes]
rs1343608	0.97[EUR][1000 genomes]
rs17053814	0.93[ASN][1000 genomes]
rs17053823	0.82[ASN][1000 genomes]
rs17053844	0.85[ASN][1000 genomes]
rs17053849	0.85[ASN][1000 genomes]
rs17053872	0.85[ASN][1000 genomes]
rs17054812	0.97[EUR][1000 genomes]
rs17054937	0.94[EUR][1000 genomes]
rs1891947	0.84[ASN][1000 genomes]
rs1909651	0.83[EUR][1000 genomes]
rs2275840	0.93[ASN][1000 genomes]
rs2799344	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2799345	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2806957	0.83[EUR][1000 genomes]
rs34030659	0.97[EUR][1000 genomes]
rs34031649	0.97[EUR][1000 genomes]
rs34059997	0.97[EUR][1000 genomes]
rs34110102	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34162017	0.94[ASN][1000 genomes]
rs34163916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34201111	0.97[EUR][1000 genomes]
rs34211399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34298498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34330988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34374288	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34531708	0.97[EUR][1000 genomes]
rs34557321	0.94[EUR][1000 genomes]
rs34610752	0.80[EUR][1000 genomes]
rs34642277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34687272	0.97[EUR][1000 genomes]
rs34756826	0.94[EUR][1000 genomes]
rs34775431	1.00[AFR][1000 genomes]
rs34820311	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34902019	0.97[EUR][1000 genomes]
rs35003538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35007240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35114755	0.97[EUR][1000 genomes]
rs35121580	0.85[ASN][1000 genomes]
rs35137422	0.92[ASN][1000 genomes]
rs35226075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35340650	0.94[EUR][1000 genomes]
rs35397855	0.85[ASN][1000 genomes]
rs35404249	1.00[AFR][1000 genomes]
rs35412628	1.00[AFR][1000 genomes]
rs35472513	0.85[ASN][1000 genomes]
rs35559066	0.89[ASN][1000 genomes]
rs35575822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35625606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35628629	0.92[EUR][1000 genomes]
rs35666947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35727089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35756659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35765587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35800707	0.94[EUR][1000 genomes]
rs36081995	0.85[ASN][1000 genomes]
rs55972529	0.97[EUR][1000 genomes]
rs57273256	0.97[EUR][1000 genomes]
rs57454139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59155861	0.86[EUR][1000 genomes]
rs59297590	0.97[EUR][1000 genomes]
rs59345770	0.85[ASN][1000 genomes]
rs59486247	1.00[AFR][1000 genomes]
rs59513810	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59960345	0.97[EUR][1000 genomes]
rs60408242	0.97[EUR][1000 genomes]
rs61950074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950078	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61950079	0.97[EUR][1000 genomes]
rs61950086	0.97[EUR][1000 genomes]
rs61950132	1.00[AFR][1000 genomes]
rs61950491	0.85[ASN][1000 genomes]
rs61950492	0.85[ASN][1000 genomes]
rs61950504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61950522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6561705	0.92[EUR][1000 genomes]
rs6561706	0.97[EUR][1000 genomes]
rs6561707	0.97[EUR][1000 genomes]
rs7320513	0.97[EUR][1000 genomes]
rs7325509	0.89[EUR][1000 genomes]
rs74086489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7998204	0.97[EUR][1000 genomes]
rs7998385	0.89[EUR][1000 genomes]
rs912053	0.89[EUR][1000 genomes]
rs9563134	0.88[EUR][1000 genomes]
rs9563136	0.94[EUR][1000 genomes]
rs9563137	0.94[EUR][1000 genomes]
rs9563138	0.94[EUR][1000 genomes]
rs9568814	0.94[EUR][1000 genomes]
rs9568815	0.94[EUR][1000 genomes]
rs9568816	0.94[EUR][1000 genomes]
rs9568817	0.94[EUR][1000 genomes]
rs9568820	0.94[EUR][1000 genomes]
rs9568821	0.94[EUR][1000 genomes]
rs9568822	0.94[EUR][1000 genomes]
rs9568823	0.94[EUR][1000 genomes]
rs9568824	0.94[EUR][1000 genomes]
rs9568825	0.94[EUR][1000 genomes]
rs9568827	0.89[EUR][1000 genomes]
rs995821	0.83[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	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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53639200-53654800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr13:53641000-53643800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:53641600-53643800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53641600-53644000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:53642200-53643800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:53642200-53643800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:53642600-53643800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr13:53643000-53644000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr13:53643000-53648200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:53643200-53643800	Enhancers	Fetal Brain Female	brain
11	chr13:53643200-53647400	Weak transcription	Brain Anterior Caudate	brain
12	chr13:53643200-53648800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:53643400-53643800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr13:53643400-53644000	Enhancers	Brain Substantia Nigra	brain
15	chr13:53643400-53647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:53643600-53643800	Enhancers	Brain Angular Gyrus	brain
17	chr13:53643600-53643800	Enhancers	Brain Hippocampus Middle	brain
18	chr13:53643600-53645400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr13:53643600-53647200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:53643600-53648000	Weak transcription	Brain Germinal Matrix	brain
21	chr13:53643600-53649600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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