Variant report

Variant	rs4985975
Chromosome Location	chr17:20972023-20972024
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1045162	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.91[AMR][1000 genomes]
rs1127814	0.91[AMR][1000 genomes]
rs11867648	0.84[MKK][hapmap]
rs11867665	0.86[ASN][1000 genomes]
rs11871072	0.86[ASN][1000 genomes]
rs12051606	0.85[AMR][1000 genomes]
rs12600703	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12601292	0.80[AMR][1000 genomes]
rs12602058	0.90[JPT][hapmap];0.94[MKK][hapmap];0.86[AMR][1000 genomes]
rs1542552	0.83[LWK][hapmap];0.94[MKK][hapmap];0.86[AMR][1000 genomes]
rs17770614	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[AMR][1000 genomes]
rs1871276	0.89[ASN][1000 genomes]
rs2054464	0.89[AMR][1000 genomes]
rs2127095	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2291034	0.95[JPT][hapmap]
rs2364326	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28502198	0.82[ASN][1000 genomes]
rs2886105	0.80[AMR][1000 genomes]
rs4445951	0.91[AMR][1000 genomes]
rs4985811	0.85[AMR][1000 genomes]
rs4985814	0.86[AMR][1000 genomes]
rs4985815	0.86[AMR][1000 genomes]
rs4985816	0.91[AMR][1000 genomes]
rs4985827	0.85[ASN][1000 genomes]
rs4985959	0.89[JPT][hapmap]
rs4985963	0.89[JPT][hapmap]
rs4985966	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985968	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4985969	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4985970	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4985971	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56323013	0.86[AMR][1000 genomes]
rs58235085	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59543297	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59713572	0.86[AMR][1000 genomes]
rs719093	0.95[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes]
rs7209129	0.89[JPT][hapmap]
rs72840147	0.84[ASN][1000 genomes]
rs872789	0.83[ASN][1000 genomes]
rs880653	0.80[AMR][1000 genomes]
rs899337	0.82[AMR][1000 genomes]
rs899340	0.89[JPT][hapmap]
rs9911289	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4985975	RP11-344E13.3	cis	lung	GTEx
rs4985975	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs4985975	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs4985975	RP11-344E13.3	cis	Whole Blood	GTEx
rs4985975	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs4985975	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs4985975	RP11-344E13.3	cis	Artery Tibial	GTEx
rs4985975	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4985975	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs4985975	RP11-344E13.3	cis	Thyroid	GTEx
rs4985975	RP11-344E13.3	cis	Stomach	GTEx
rs4985975	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20967400-20973000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:20969200-20972600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:20970200-20978600	Weak transcription	HSMMtube	muscle
4	chr17:20970400-20972800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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