Variant report

Variant	rs3826659
Chromosome Location	chr19:51891909-51891910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr19:51891885-51892135	GM12878	blood:	n/a	chr19:51892107-51892116 chr19:51892107-51892116

No.	Distal block	Cell Line	Cell type
1	chr19:51859965..51862618-chr19:51891276..51893885,2	K562	blood:
2	chr19:51841717..51843747-chr19:51891710..51894546,2	K562	blood:
3	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:
4	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:

Variant related genes	Relation type
LIM2	TF binding region
ENSG00000105379	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000268889	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10404198	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10419880	0.92[ASN][1000 genomes]
rs11084075	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084076	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084077	0.94[ASN][1000 genomes]
rs11669975	0.88[ASN][1000 genomes]
rs11670065	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11673263	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2411321	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2411322	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547308	0.98[ASN][1000 genomes]
rs2547309	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2741240	0.95[ASN][1000 genomes]
rs2741241	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810093	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810094	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810095	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810096	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810097	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826658	0.99[ASN][1000 genomes]
rs3826660	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826662	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3826663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826665	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377257	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4441376	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250926	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251238	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251311	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251566	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257275	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7508570	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8100861	0.88[ASN][1000 genomes]
rs8104425	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107533	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111906	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv14170	chr19:51891298-51892818	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3826659	CTD-2616J11.4	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51872000-51897000	Weak transcription	Right Atrium	heart
2	chr19:51887800-51893400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:51889200-51893600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:51889200-51893800	Weak transcription	GM12878-XiMat	blood
5	chr19:51889200-51897000	Weak transcription	Spleen	Spleen
6	chr19:51889400-51893000	Weak transcription	K562	blood
7	chr19:51890200-51892600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:51890200-51893000	Flanking Active TSS	HepG2	liver
9	chr19:51890200-51893200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:51890400-51892000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:51890800-51892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:51891000-51894400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:51891000-51897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:51891200-51892600	Enhancers	Fetal Intestine Small	intestine
15	chr19:51891200-51894200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:51891600-51892000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr19:51891600-51892400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:51891600-51892600	Enhancers	Fetal Intestine Large	intestine
19	chr19:51891600-51897000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:51891800-51892800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr19:51891800-51894000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:51891800-51897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:51891800-51897000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:51891800-51897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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