Variant report

Variant	rs10165862
Chromosome Location	chr2:73610743-73610744
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	chr2:73494646..73496647-chr2:73610262..73612844,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10175529	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184268	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10189574	0.80[AFR][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10193972	0.80[YRI][hapmap]
rs10206188	0.83[ASN][1000 genomes]
rs10496191	0.81[AMR][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs11126395	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11126396	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11126399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11689392	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11693531	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11898362	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11901272	1.00[YRI][hapmap]
rs12465867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1403412	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]
rs1406105	0.91[CHB][hapmap]
rs1522926	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1534471	0.80[YRI][hapmap];0.84[AMR][1000 genomes]
rs1851546	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1852644	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1881246	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1881247	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2017116	1.00[CHB][hapmap]
rs2037814	1.00[CHB][hapmap]
rs2091022	0.81[ASN][1000 genomes]
rs2421489	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2421545	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2421550	0.80[YRI][hapmap];0.84[AMR][1000 genomes]
rs2901437	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2901438	0.81[AMR][1000 genomes]
rs35885918	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813227	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3820700	1.00[CHB][hapmap]
rs6546824	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap]
rs6546837	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6546838	0.81[AMR][1000 genomes]
rs6546839	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707722	0.83[AMR][1000 genomes]
rs6710659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6716776	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724782	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6728128	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6740223	0.83[AMR][1000 genomes]
rs6741067	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6747145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6756987	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7560272	0.83[ASN][1000 genomes]
rs7566385	0.80[AFR][1000 genomes]
rs7567017	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567343	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7576824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7585004	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7598946	0.82[AFR][1000 genomes]
rs7604588	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs780390	1.00[CHB][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10165862	ALMS1	cis	Whole Blood	GTEx
rs10165862	ALMS1P	cis	Whole Blood	GTEx
rs10165862	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs10165862	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 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	chr2:73610400-73610800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:73610400-73610800	Bivalent Enhancer	HepG2	liver
4	chr2:73610600-73610800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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