Variant report

Variant	rs2048949
Chromosome Location	chr2:99544518-99544519
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	chr2:99532387..99535858-chr2:99543640..99546629,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10192266	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712042	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712043	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13005124	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13006398	0.81[EUR][1000 genomes]
rs13024838	0.84[EUR][1000 genomes]
rs13028500	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1607256	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17758170	0.84[EUR][1000 genomes]
rs1878589	0.83[EUR][1000 genomes]
rs1949424	0.80[EUR][1000 genomes]
rs4311103	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4850890	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4851174	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851175	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851176	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851177	0.83[AMR][1000 genomes]
rs6419564	0.83[AMR][1000 genomes]
rs6542843	0.83[AMR][1000 genomes]
rs6542845	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6724477	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739176	0.83[AMR][1000 genomes]
rs6739503	0.83[AMR][1000 genomes]
rs6741166	0.84[EUR][1000 genomes]
rs6742047	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752025	0.82[EUR][1000 genomes]
rs7423519	0.84[EUR][1000 genomes]
rs7565819	0.84[EUR][1000 genomes]
rs7588441	0.84[EUR][1000 genomes]
rs7593332	0.80[EUR][1000 genomes]
rs908672	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2048949	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2048949	LIPT1	cis	Esophagus Mucosa	GTEx
rs2048949	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99538000-99550800	Weak transcription	Gastric	stomach
2	chr2:99538400-99551400	Weak transcription	Esophagus	oesophagus
3	chr2:99542800-99545000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:99543000-99548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:99543600-99545400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:99543600-99545400	Weak transcription	A549	lung
7	chr2:99543800-99545600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:99543800-99551200	Weak transcription	HMEC	breast
9	chr2:99543800-99551400	Weak transcription	Pancreas	Pancrea
10	chr2:99544000-99549600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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