Variant report

Variant	rs6872395
Chromosome Location	chr5:52847798-52847799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10043710	0.85[ASN][1000 genomes]
rs10513019	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11740800	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11743262	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs16881514	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs16881524	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs16881561	1.00[JPT][hapmap]
rs2087618	0.82[YRI][hapmap]
rs28855127	0.80[ASN][1000 genomes]
rs3958630	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs4147735	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4147739	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4147744	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs4618398	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748137	0.86[ASN][1000 genomes]
rs72750138	0.82[ASN][1000 genomes]
rs7729894	0.86[CHB][hapmap];1.00[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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6872395	PPAP2A	cis	parietal	SCAN
rs6872395	ARL15	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52842600-52849000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:52843400-52848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:52843600-52848600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:52843600-52850600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:52844800-52848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52845000-52848800	Weak transcription	Stomach Mucosa	stomach
7	chr5:52846000-52848000	Weak transcription	K562	blood

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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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