Variant report

Variant	rs520406
Chromosome Location	chr3:155248859-155248860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1084714	0.93[ASN][1000 genomes]
rs168601	0.94[ASN][1000 genomes]
rs173384	0.94[ASN][1000 genomes]
rs359541	0.94[ASN][1000 genomes]
rs359543	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs359544	0.94[ASN][1000 genomes]
rs359545	0.94[ASN][1000 genomes]
rs359546	0.88[ASN][1000 genomes]
rs359560	0.83[ASN][1000 genomes]
rs4679748	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680190	0.95[ASN][1000 genomes]
rs498378	0.86[ASN][1000 genomes]
rs499014	0.93[ASN][1000 genomes]
rs525486	0.95[ASN][1000 genomes]
rs529325	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533168	0.92[ASN][1000 genomes]
rs545255	0.95[ASN][1000 genomes]
rs592982	0.95[ASN][1000 genomes]
rs595076	0.95[ASN][1000 genomes]
rs596578	0.95[ASN][1000 genomes]
rs597718	0.95[ASN][1000 genomes]
rs610514	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629698	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441000	0.92[ASN][1000 genomes]
rs673417	0.95[ASN][1000 genomes]
rs6777148	0.92[ASN][1000 genomes]
rs687462	0.92[ASN][1000 genomes]
rs7636015	0.81[ASN][1000 genomes]
rs783549	0.92[ASN][1000 genomes]
rs783552	0.93[ASN][1000 genomes]
rs783553	0.92[ASN][1000 genomes]
rs9289956	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763309	chr3:155193454-155256770	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr3:155200800-155251400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:155230600-155249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155230600-155271400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:155231200-155253000	Weak transcription	A549	lung
5	chr3:155232200-155253000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:155232200-155258800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:155232200-155274000	Weak transcription	Pancreas	Pancrea
8	chr3:155232400-155250400	Weak transcription	Gastric	stomach
9	chr3:155235400-155249000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:155236200-155249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:155238000-155249000	Strong transcription	Dnd41	blood
12	chr3:155241800-155249000	Weak transcription	Fetal Thymus	thymus
13	chr3:155241800-155273000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:155244800-155249800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:155244800-155258800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:155245000-155249000	Weak transcription	Thymus	Thymus
17	chr3:155247200-155253000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:155248400-155250400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:155248400-155260000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:155248600-155249200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:155248600-155250600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr3:155248800-155249200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:155248800-155249600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr3:155248800-155249800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr3:155248800-155250400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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