Variant report

Variant	rs891898
Chromosome Location	chr5:146620082-146620083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1432646	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1432647	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545027	0.87[JPT][hapmap]
rs2400281	0.87[ASN][1000 genomes]
rs4705026	0.87[JPT][hapmap]
rs4705027	0.87[JPT][hapmap]
rs4705028	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs4705132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705139	0.87[JPT][hapmap]
rs4705141	0.90[AFR][1000 genomes]
rs6580455	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs6874352	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717260	0.92[JPT][hapmap]
rs9687342	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv819857	chr5:146619761-146623148	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs891898	PCYOX1L	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146615000-146620800	Weak transcription	Psoas Muscle	Psoas
2	chr5:146615000-146621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:146615200-146621400	Weak transcription	Aorta	Aorta
4	chr5:146616400-146628000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:146619000-146624200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:146619400-146620400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:146619600-146620200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:146619600-146620400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:146619800-146620200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:146619800-146620200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:146619800-146620400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:146619800-146620400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:146619800-146620400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:146619800-146620400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:146619800-146620600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:146620000-146620400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:146620000-146621600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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