Variant report

Variant	rs16972405
Chromosome Location	chr15:42284800-42284801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42283450..42285988-chr15:42370999..42373480,2	K562	blood:
2	chr15:42284477..42286944-chr15:42348245..42350387,2	MCF-7	breast:
3	chr15:42284094..42286623-chr15:42288383..42290349,2	K562	blood:
4	chr15:42279659..42283459-chr15:42284421..42285935,3	K562	blood:

Variant related genes	Relation type
ENSG00000188089	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12102194	1.00[EUR][1000 genomes]
rs16972239	1.00[EUR][1000 genomes]
rs16972253	1.00[EUR][1000 genomes]
rs16972264	1.00[EUR][1000 genomes]
rs16972274	1.00[EUR][1000 genomes]
rs16972281	1.00[EUR][1000 genomes]
rs16972286	1.00[EUR][1000 genomes]
rs16972704	1.00[EUR][1000 genomes]
rs16972772	1.00[EUR][1000 genomes]
rs16972775	1.00[EUR][1000 genomes]
rs17842096	1.00[EUR][1000 genomes]
rs28626380	1.00[EUR][1000 genomes]
rs34424865	1.00[EUR][1000 genomes]
rs34807597	1.00[EUR][1000 genomes]
rs36126315	1.00[EUR][1000 genomes]
rs61741913	1.00[EUR][1000 genomes]
rs61748710	1.00[EUR][1000 genomes]
rs61753581	1.00[EUR][1000 genomes]
rs7173832	1.00[EUR][1000 genomes]
rs7176585	1.00[EUR][1000 genomes]
rs7177717	1.00[EUR][1000 genomes]
rs7180290	1.00[EUR][1000 genomes]
rs7182959	1.00[EUR][1000 genomes]
rs919142	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
5	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16972405	LAPTM4B	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42273000-42301800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:42273200-42288000	Weak transcription	Lung	lung
3	chr15:42273800-42290000	Weak transcription	Right Atrium	heart
4	chr15:42273800-42301800	Weak transcription	Esophagus	oesophagus
5	chr15:42276200-42287000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42282200-42287000	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:42282800-42287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:42283200-42291600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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