Variant report

Variant	rs10863254
Chromosome Location	chr1:216730387-216730388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10495031	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10779279	1.00[LWK][hapmap]
rs10863253	0.86[ASW][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.81[AFR][1000 genomes]
rs10863255	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863257	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11117619	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11117622	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11117623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11117625	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11117632	0.91[AFR][1000 genomes]
rs11117633	1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs11117637	0.86[ASW][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs11117638	0.81[AFR][1000 genomes]
rs11117639	0.81[AFR][1000 genomes]
rs11572727	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs11581434	0.91[AFR][1000 genomes]
rs11585397	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11587086	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11590373	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12120908	1.00[LWK][hapmap]
rs12122051	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs12123789	1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs12127486	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12128352	0.81[AFR][1000 genomes]
rs12129039	0.91[AFR][1000 genomes]
rs12131827	0.81[AFR][1000 genomes]
rs12132004	0.81[AFR][1000 genomes]
rs12133226	1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs12138981	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12140540	0.91[AFR][1000 genomes]
rs12141843	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12145447	0.91[AFR][1000 genomes]
rs17669502	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17671012	0.91[AFR][1000 genomes]
rs1984137	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2030059	0.85[JPT][hapmap]
rs2047430	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2173371	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs35079003	0.91[AFR][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	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv4565	chr1:216720070-216765053	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10863254	PROX1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216705400-216734800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:216708800-216744600	Weak transcription	Left Ventricle	heart
3	chr1:216721800-216774000	Weak transcription	Placenta	Placenta
4	chr1:216729200-216733800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:216729400-216733800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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