Variant report

Variant	rs7604588
Chromosome Location	chr2:73571417-73571418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10165862	0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10175529	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10206188	0.83[ASN][1000 genomes]
rs1083922	0.86[CHD][hapmap]
rs10865398	0.86[CHD][hapmap]
rs11126395	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126396	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126399	0.86[EUR][1000 genomes]
rs11693531	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11898362	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12465867	0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403412	0.90[CEU][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1522926	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1851546	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1852644	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2091022	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421489	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2901437	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35885918	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820700	0.83[CHD][hapmap]
rs6546824	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546827	0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546829	0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706235	0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706409	0.83[CHD][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6710659	0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6716776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728128	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6747145	0.84[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748040	0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6749680	0.86[CHD][hapmap]
rs7560272	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567017	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7567343	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7573275	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs7576824	0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780390	0.83[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013190	chr2:73489679-73572643	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7604588	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs7604588	LRRTM4	cis	cerebellum	SCAN
rs7604588	ALMS1P	cis	cerebellum	SCAN
rs7604588	EXOC6B	cis	cerebellum	SCAN
rs7604588	ALMS1P	cis	parietal	SCAN
rs7604588	TLX2	cis	cerebellum	SCAN
rs7604588	ALMS1	cis	parietal	SCAN
rs7604588	ALMS1	cis	Whole Blood	GTEx
rs7604588	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs7604588	ALMS1P	cis	Whole Blood	GTEx
rs7604588	ALMS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73571000-73571600	Bivalent Enhancer	HepG2	liver

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