Variant report

Variant	rs4985811
Chromosome Location	chr17:20893572-20893573
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	chr17:20893363..20896072-chr17:20898999..20901703,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1045162	0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1127814	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12051606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600703	0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs12601292	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12602058	0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1531566	0.91[ASN][1000 genomes]
rs1542552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17770614	0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2054464	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2127095	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2291034	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2364326	0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2886105	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4445951	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985815	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985816	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985959	0.95[JPT][hapmap]
rs4985963	0.95[JPT][hapmap]
rs4985966	0.90[AMR][1000 genomes]
rs4985968	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985969	0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985970	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985971	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985975	0.85[AMR][1000 genomes]
rs56209912	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56234441	0.82[ASN][1000 genomes]
rs56323013	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58235085	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59543297	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59713572	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719093	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7209129	0.95[JPT][hapmap]
rs8069159	1.00[YRI][hapmap]
rs880653	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs899337	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs899340	0.95[JPT][hapmap]
rs9911289	0.95[JPT][hapmap]

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	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	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
3	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
rs4985811	RP11-344E13.3	cis	lung	GTEx
rs4985811	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs4985811	RP11-344E13.3	cis	Artery Tibial	GTEx
rs4985811	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs4985811	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs4985811	RP11-344E13.3	cis	Whole Blood	GTEx
rs4985811	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4985811	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs4985811	RP11-344E13.3	cis	Stomach	GTEx
rs4985811	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs4985811	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs4985811	RP11-344E13.3	cis	Thyroid	GTEx

Chromatin state (count:25 , 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	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
3	chr17:20881400-20896200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr17:20886800-20896400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:20887000-20896600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr17:20887200-20896000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:20891000-20897400	Weak transcription	Gastric	stomach
8	chr17:20892000-20895800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:20892400-20895800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:20892800-20894000	Enhancers	Fetal Muscle Trunk	muscle
11	chr17:20892800-20894200	Enhancers	Fetal Stomach	stomach
12	chr17:20892800-20895000	Enhancers	HepG2	liver
13	chr17:20893000-20893800	Enhancers	Esophagus	oesophagus
14	chr17:20893000-20893800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr17:20893000-20894200	Enhancers	Fetal Muscle Leg	muscle
16	chr17:20893000-20894200	Bivalent Enhancer	Placenta	Placenta
17	chr17:20893000-20901600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr17:20893200-20894000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:20893200-20894000	Enhancers	HSMMtube	muscle
20	chr17:20893200-20895400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:20893400-20893600	Enhancers	Pancreas	Pancrea
22	chr17:20893400-20893800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:20893400-20894200	Enhancers	Colon Smooth Muscle	Colon
24	chr17:20893400-20894200	Enhancers	Fetal Heart	heart
25	chr17:20893400-20895400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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