Variant report

Variant	rs6752025
Chromosome Location	chr2:99505699-99505700
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	chr2:99505531..99508517-chr2:99513277..99515165,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10169003	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10175560	0.83[EUR][1000 genomes]
rs10181972	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10192266	0.85[EUR][1000 genomes]
rs11123756	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11887536	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11900176	0.83[EUR][1000 genomes]
rs11900524	0.83[EUR][1000 genomes]
rs12478574	0.93[EUR][1000 genomes]
rs12712033	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712034	0.85[EUR][1000 genomes]
rs12712037	0.82[EUR][1000 genomes]
rs12712039	0.86[AFR][1000 genomes]
rs12712040	0.90[EUR][1000 genomes]
rs12712042	0.86[EUR][1000 genomes]
rs12990579	0.83[EUR][1000 genomes]
rs12992214	0.81[ASN][1000 genomes]
rs13004923	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13005124	0.85[EUR][1000 genomes]
rs13005148	0.90[EUR][1000 genomes]
rs13006398	0.81[EUR][1000 genomes]
rs13024838	0.86[EUR][1000 genomes]
rs13028500	0.83[EUR][1000 genomes]
rs1581249	0.90[EUR][1000 genomes]
rs1581250	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17758170	0.86[EUR][1000 genomes]
rs1878585	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1878589	0.85[EUR][1000 genomes]
rs1949424	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962029	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2048949	0.82[EUR][1000 genomes]
rs4311103	0.84[EUR][1000 genomes]
rs4499468	0.93[EUR][1000 genomes]
rs4553869	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4850890	0.86[EUR][1000 genomes]
rs4851174	0.85[EUR][1000 genomes]
rs4851175	0.85[EUR][1000 genomes]
rs4851176	0.86[EUR][1000 genomes]
rs6542841	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6542845	0.85[EUR][1000 genomes]
rs6704682	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6724477	0.85[EUR][1000 genomes]
rs6726156	0.84[ASN][1000 genomes]
rs6739097	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741166	0.86[EUR][1000 genomes]
rs6742047	0.86[EUR][1000 genomes]
rs6757098	0.93[EUR][1000 genomes]
rs6760065	0.93[EUR][1000 genomes]
rs7423519	0.86[EUR][1000 genomes]
rs7565510	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7565614	0.83[EUR][1000 genomes]
rs7565736	0.82[EUR][1000 genomes]
rs7565819	0.86[EUR][1000 genomes]
rs7588441	0.86[EUR][1000 genomes]
rs7590596	0.90[EUR][1000 genomes]
rs7593332	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883773	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2277586	chr2:99505561-99505989	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6752025	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99500000-99517000	Weak transcription	Gastric	stomach

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