Variant report

Variant	rs1403412
Chromosome Location	chr2:73598092-73598093
allele	A/G
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	chr2:73596191..73598481-chr2:73612504..73614239,2	K562	blood:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10165862	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10175529	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10184268	0.82[AMR][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs10193972	1.00[YRI][hapmap]
rs10206188	0.86[ASN][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs10865398	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs11126395	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11126396	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11126399	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11689392	0.84[AMR][1000 genomes]
rs11693531	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898362	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465867	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs1522926	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534471	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1851546	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1852644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap]
rs1881246	1.00[CHB][hapmap]
rs1881247	1.00[CHB][hapmap]
rs2017116	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs2037814	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2056486	1.00[YRI][hapmap]
rs2091022	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421489	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2421545	1.00[CHB][hapmap]
rs2421546	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2421550	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2901437	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885918	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs6546824	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546826	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]
rs6546827	0.89[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546829	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap]
rs6546838	1.00[YRI][hapmap]
rs6706235	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6706409	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6710659	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6716776	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6728128	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741067	0.81[AMR][1000 genomes]
rs6747145	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748040	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.94[CHD][hapmap]
rs7560272	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7567017	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7567343	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573275	0.83[ASN][1000 genomes]
rs7574291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs7576824	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]
rs7598901	0.92[CHB][hapmap];0.88[CHD][hapmap];0.80[MEX][hapmap]
rs7604588	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs780396	1.00[CHB][hapmap]

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	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
2	nsv961794	chr2:73596795-73598813	Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1403412	ALMS1	cis	cerebellum	SCAN
rs1403412	ALMS1	cis	parietal	SCAN
rs1403412	LRRTM4	cis	cerebellum	SCAN
rs1403412	ALMS1P	cis	parietal	SCAN
rs1403412	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs1403412	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1403412	ALMS1P	cis	Whole Blood	GTEx
rs1403412	PAIP2B	cis	cerebellum	SCAN
rs1403412	ALMS1	cis	normal skin	skin_eQTL
rs1403412	ALMS1P	cis	cerebellum	SCAN

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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