Variant report

Variant	rs10048757
Chromosome Location	chr2:212249836-212249837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11895168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475523	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13014117	0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025037	0.99[ASN][1000 genomes]
rs1583483	0.91[ASN][1000 genomes]
rs1595062	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595065	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1816533	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821656	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836724	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1972820	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2033648	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2076818	0.81[YRI][hapmap]
rs3791692	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs3828243	0.83[JPT][hapmap]
rs4672612	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4673610	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4673615	0.87[ASN][1000 genomes]
rs6710253	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6728196	0.90[ASN][1000 genomes]
rs7571245	0.89[EUR][1000 genomes]
rs934607	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][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	nsv834523	chr2:212163236-212331393	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv875776	chr2:212196908-212264818	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv584314	chr2:212238982-212292521	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv460065	chr2:212244520-212276710	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
5	nsv584315	chr2:212244520-212276710	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10048757	PIKFYVE	cis	parietal	SCAN
rs10048757	PTH2R	cis	parietal	SCAN
rs10048757	KLF7	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212244000-212254800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:212244200-212253800	Weak transcription	Fetal Heart	heart
3	chr2:212245800-212256800	Weak transcription	Psoas Muscle	Psoas
4	chr2:212246800-212255400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:212248000-212255200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:212248800-212250600	Weak transcription	Aorta	Aorta
7	chr2:212248800-212252200	Weak transcription	Pancreas	Pancrea
8	chr2:212249600-212250200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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