Variant report

Variant	rs6546826
Chromosome Location	chr2:73599808-73599809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73597856..73600814-chr2:73611443..73614137,4	MCF-7	breast:
2	chr2:73597000..73599124-chr2:73599512..73601523,2	K562	blood:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction
ENSG00000214484	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10165862	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10175529	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs1083922	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs10865398	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs11126395	0.83[EUR][1000 genomes]
rs11126396	0.83[EUR][1000 genomes]
rs11126399	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs11693531	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11898362	0.82[EUR][1000 genomes]
rs12465867	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1403412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs1522926	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1851546	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1852644	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap]
rs1881246	1.00[CHB][hapmap]
rs1881247	1.00[CHB][hapmap]
rs2017116	1.00[CHB][hapmap]
rs2037814	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2091022	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421489	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2421545	1.00[CHB][hapmap]
rs2421546	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2901437	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35885918	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs6546824	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546827	0.89[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546829	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap]
rs6706235	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6706409	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6710659	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716776	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6728128	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747145	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748040	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.97[CHD][hapmap]
rs7560272	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7567017	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567343	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573275	0.83[EUR][1000 genomes]
rs7574291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs7576824	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]
rs7580825	0.91[YRI][hapmap]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7604588	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs780396	1.00[CHB][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6546826	PAIP2B	cis	cerebellum	SCAN
rs6546826	LRRTM4	cis	cerebellum	SCAN
rs6546826	ALMS1	cis	cerebellum	SCAN
rs6546826	ALMS1	cis	parietal	SCAN
rs6546826	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6546826	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6546826	ALMS1	cis	Whole Blood	GTEx
rs6546826	ALMS1P	cis	cerebellum	SCAN
rs6546826	ALMS1P	cis	Whole Blood	GTEx
rs6546826	ALMS1P	cis	Nerve Tibial	GTEx
rs6546826	ALMS1P	cis	parietal	SCAN
rs6546826	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546826	ALMS1	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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