Variant report

Variant	rs2165988
Chromosome Location	chr10:117028264-117028265
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10787567	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10787573	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11197173	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11498596	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12253499	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1264750	0.88[AMR][1000 genomes]
rs1264755	0.84[EUR][1000 genomes]
rs1264764	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264770	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs1264773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs1264781	0.87[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs1264798	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269601	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1494174	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1565833	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs1615076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1889610	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs2201363	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2256563	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2485966	0.84[ASN][1000 genomes]
rs2485968	0.83[ASN][1000 genomes]
rs2485971	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs2587461	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs584030	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs594160	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs615905	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs649292	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs650060	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs675816	0.81[EUR][1000 genomes]
rs679986	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs9630104	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9630105	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869279	chr10:116884639-117032437	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv868940	chr10:116933802-117032437	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2165988	PRLHR	cis	parietal	SCAN
rs2165988	EIF3A	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116997200-117049800	Weak transcription	Ovary	ovary
2	chr10:117011400-117034400	Weak transcription	Aorta	Aorta
3	chr10:117019000-117034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:117019000-117034600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr10:117023400-117032000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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