Variant report

Variant	rs7576824
Chromosome Location	chr2:73611281-73611282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr2:73611249-73611375	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73494646..73496647-chr2:73610262..73612844,2	MCF-7	breast:

Variant related genes	Relation type
ALMS1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10165862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10175529	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs1083922	0.84[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs11126395	0.82[ASN][1000 genomes]
rs11126396	0.82[ASN][1000 genomes]
rs11126399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693531	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898362	0.82[ASN][1000 genomes]
rs12465867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs1522926	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1851546	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1852644	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1881246	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1881247	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2037814	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2091022	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421489	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2421545	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2901437	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35885918	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs6546824	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716776	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6728128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs7560272	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7567017	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567343	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7573275	0.83[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7604588	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs780396	1.00[CHB][hapmap];0.80[JPT][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	nsv2778	chr2:73596272-73615138	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7576824	ALMS1P	cis	cerebellum	SCAN
rs7576824	LRRTM4	cis	cerebellum	SCAN
rs7576824	ALMS1P	cis	Whole Blood	GTEx
rs7576824	ALMS1	cis	Whole Blood	GTEx
rs7576824	ALMS1	cis	parietal	SCAN
rs7576824	ALMS1	cis	multi-tissue	Pritchard
rs7576824	ALMS1	cis	cerebellum	SCAN
rs7576824	PAIP2B	cis	cerebellum	SCAN
rs7576824	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs7576824	ALMS1P	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73610000-73612000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:73610800-73611400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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