Variant report

Variant	rs1542552
Chromosome Location	chr17:20885395-20885396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20839289..20841675-chr17:20882909..20885590,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-5	chr17:20884800-20885670	ENSG00000264660.1

Variant related genes	Relation type
ENSG00000265099	Chromatin interaction

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

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

rs_ID	r²[population]
rs1045162	0.87[CHD][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1127814	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11867648	0.89[MKK][hapmap]
rs12051606	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12600703	0.82[MKK][hapmap];0.86[AMR][1000 genomes]
rs12601292	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12602058	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1531566	0.86[ASN][1000 genomes]
rs17770614	0.84[CHD][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes]
rs2054464	0.93[AMR][1000 genomes]
rs2127095	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2291034	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs2364326	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2886105	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4445951	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985811	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985814	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985815	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985816	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985966	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4985968	0.89[AMR][1000 genomes]
rs4985969	0.87[CHD][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4985970	0.92[AMR][1000 genomes]
rs4985971	0.88[AMR][1000 genomes]
rs4985975	0.86[AMR][1000 genomes]
rs56209912	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56323013	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58235085	0.92[AMR][1000 genomes]
rs59543297	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs59713572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs719093	0.95[AMR][1000 genomes]
rs880653	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899337	0.88[CEU][hapmap];0.90[AFR][1000 genomes];0.95[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
rs1542552	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs1542552	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs1542552	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs1542552	RP11-344E13.3	cis	Whole Blood	GTEx
rs1542552	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs1542552	RP11-344E13.3	cis	Thyroid	GTEx
rs1542552	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs1542552	RP11-344E13.3	cis	Stomach	GTEx
rs1542552	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1542552	RP11-344E13.3	cis	lung	GTEx
rs1542552	RP11-344E13.3	cis	Artery Tibial	GTEx
rs1542552	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:16 , 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	chr17:20862600-20890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:20866000-20886600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:20871800-20886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:20873200-20886400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:20873200-20890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
8	chr17:20881400-20896200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr17:20882200-20886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:20882800-20887400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:20883200-20885800	Strong transcription	HepG2	liver
12	chr17:20883800-20886600	Weak transcription	K562	blood
13	chr17:20884800-20885400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:20884800-20887200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:20885000-20887200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:20885200-20885400	Enhancers	Skeletal Muscle Male	skeletal muscle

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