Variant report

Variant	rs11644887
Chromosome Location	chr16:48488359-48488360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48481663..48485159-chr16:48487604..48489866,3	K562	blood:
2	chr16:48486381..48489610-chr16:48544436..48547308,3	MCF-7	breast:
3	chr16:48486870..48489852-chr16:48492927..48494661,2	K562	blood:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction
ENSG00000261802	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11643514	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11648225	0.80[ASN][1000 genomes]
rs11865776	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1566466	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1566467	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062553	0.80[ASN][1000 genomes]
rs2088753	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2088754	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4785244	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4785520	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55745119	0.83[ASN][1000 genomes]
rs56207849	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7184700	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194822	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7198215	0.95[ASN][1000 genomes]
rs7198420	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203475	0.92[ASN][1000 genomes]
rs8052026	0.80[ASN][1000 genomes]
rs8054696	0.95[ASN][1000 genomes]
rs8056201	0.80[ASN][1000 genomes]
rs8056346	0.80[ASN][1000 genomes]
rs8063059	0.80[ASN][1000 genomes]
rs9888862	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9889065	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9889067	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9921402	0.80[ASN][1000 genomes]
rs9923092	0.86[ASN][1000 genomes]
rs9926683	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9933892	0.80[ASN][1000 genomes]
rs9939368	0.83[ASN][1000 genomes]
rs9940599	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9941289	0.81[EUR][1000 genomes];0.86[ASN][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	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv519663	chr16:48479935-48489387	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11644887	LONP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48485000-48491600	Weak transcription	HMEC	breast
2	chr16:48485600-48492200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:48486400-48488400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr16:48486800-48488400	Enhancers	Hela-S3	cervix
5	chr16:48487400-48491800	Weak transcription	HSMM	muscle
6	chr16:48487600-48491600	Weak transcription	Psoas Muscle	Psoas
7	chr16:48487600-48492600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:48488200-48495400	Enhancers	Primary B cells from peripheral blood	blood

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