Variant report

Variant	rs2886105
Chromosome Location	chr17:20879588-20879589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1045162	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1127814	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12051606	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12600703	0.80[AMR][1000 genomes]
rs12601292	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602058	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1531566	0.84[ASN][1000 genomes]
rs1542552	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17770614	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2054464	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2127095	0.86[AMR][1000 genomes]
rs2364326	0.86[AMR][1000 genomes]
rs4445951	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4985811	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985814	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985815	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985816	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985966	0.86[AMR][1000 genomes]
rs4985968	0.83[AMR][1000 genomes]
rs4985969	0.86[AMR][1000 genomes]
rs4985970	0.86[AMR][1000 genomes]
rs4985971	0.81[AMR][1000 genomes]
rs4985975	0.80[AMR][1000 genomes]
rs56209912	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56234441	0.82[AMR][1000 genomes]
rs56298745	0.82[AMR][1000 genomes]
rs56323013	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58235085	0.86[AMR][1000 genomes]
rs59543297	0.86[AMR][1000 genomes]
rs59713572	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719093	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs880653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899337	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2886105	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs2886105	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs2886105	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs2886105	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs2886105	RP11-344E13.3	cis	lung	GTEx
rs2886105	RP11-344E13.3	cis	Thyroid	GTEx
rs2886105	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs2886105	RP11-344E13.3	cis	Stomach	GTEx
rs2886105	RP11-344E13.3	cis	Artery Tibial	GTEx
rs2886105	RP11-344E13.3	cis	Whole Blood	GTEx
rs2886105	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2886105	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20852800-20882600	Weak transcription	K562	blood
3	chr17:20859000-20881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:20862600-20890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:20866000-20886600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20868000-20884800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:20869600-20880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:20870000-20883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20870600-20880400	Weak transcription	HepG2	liver
10	chr17:20871800-20886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:20873200-20886400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr17:20873200-20890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
14	chr17:20875400-20881000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr17:20878200-20879800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:20878200-20879800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:20878200-20879800	Enhancers	HMEC	breast
18	chr17:20878200-20879800	Enhancers	NHEK	skin
19	chr17:20878600-20879800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:20878800-20880400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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