Variant report

Variant	rs6741166
Chromosome Location	chr2:99534926-99534927
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99528371..99530987-chr2:99533577..99536633,3	MCF-7	breast:
2	chr2:99532387..99535858-chr2:99543640..99546629,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10175560	0.82[EUR][1000 genomes]
rs10192266	0.87[EUR][1000 genomes]
rs11123756	0.92[EUR][1000 genomes]
rs11900176	0.82[EUR][1000 genomes]
rs11900524	0.82[EUR][1000 genomes]
rs12464134	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12467504	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12478574	0.92[EUR][1000 genomes]
rs12712034	0.85[EUR][1000 genomes]
rs12712037	0.82[EUR][1000 genomes]
rs12712040	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712042	0.88[EUR][1000 genomes]
rs12990579	0.82[EUR][1000 genomes]
rs13005124	0.87[EUR][1000 genomes]
rs13005148	0.90[EUR][1000 genomes]
rs13006398	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024838	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13028500	0.85[EUR][1000 genomes]
rs1581249	0.91[EUR][1000 genomes]
rs17758170	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878589	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949424	0.84[EUR][1000 genomes]
rs1962029	0.92[EUR][1000 genomes]
rs2048949	0.84[EUR][1000 genomes]
rs4311103	0.87[EUR][1000 genomes]
rs4499468	0.92[EUR][1000 genomes]
rs4553869	0.92[EUR][1000 genomes]
rs4850890	0.88[EUR][1000 genomes]
rs4851174	0.88[EUR][1000 genomes]
rs4851175	0.87[EUR][1000 genomes]
rs4851176	0.88[EUR][1000 genomes]
rs6542841	0.92[EUR][1000 genomes]
rs6542845	0.87[EUR][1000 genomes]
rs6704682	0.92[EUR][1000 genomes]
rs6724477	0.87[EUR][1000 genomes]
rs6742047	0.88[EUR][1000 genomes]
rs6752025	0.86[EUR][1000 genomes]
rs6757098	0.92[EUR][1000 genomes]
rs6760065	0.92[EUR][1000 genomes]
rs7423519	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7565510	0.92[EUR][1000 genomes]
rs7565614	0.82[EUR][1000 genomes]
rs7565736	0.81[EUR][1000 genomes]
rs7565819	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7588441	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7590596	0.90[EUR][1000 genomes]
rs7593332	0.84[EUR][1000 genomes]
rs883773	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6741166	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99531200-99539000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99532000-99537400	Weak transcription	Gastric	stomach
3	chr2:99532400-99542800	Weak transcription	Pancreas	Pancrea
4	chr2:99533600-99536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:99533600-99536800	Weak transcription	Esophagus	oesophagus
6	chr2:99534000-99536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:99534000-99536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:99534200-99537000	Weak transcription	NHEK	skin
9	chr2:99534200-99539000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:99534400-99536200	Weak transcription	HMEC	breast
11	chr2:99534400-99536800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:99534400-99537400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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