Variant report

Variant	rs2252565
Chromosome Location	chr4:120613111-120613112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11722624	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11734863	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17005489	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2248806	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2250346	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2252621	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2252625	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2256054	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583596	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583597	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583604	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583605	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583608	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2583616	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2583617	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2583619	0.83[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2714960	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2714961	0.85[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2714970	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2714973	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2714976	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2714978	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2714980	0.84[AMR][1000 genomes]
rs2715026	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4834806	0.84[EUR][1000 genomes]
rs6836219	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs725449	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7437666	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2760816	chr4:120609268-120614296	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252565	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120612800-120613400	Enhancers	NHLF	lung
2	chr4:120612800-120614200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120612800-120614200	Enhancers	Osteobl	bone
4	chr4:120612800-120615600	Enhancers	NHDF-Ad	bronchial
5	chr4:120613000-120613200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:120613000-120613200	Enhancers	Fetal Muscle Leg	muscle
7	chr4:120613000-120613400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:120613000-120613600	Enhancers	Colon Smooth Muscle	Colon
9	chr4:120613000-120614000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:120613000-120614000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:120613000-120614400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:120613000-120614600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:120613000-120615000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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