Variant report

Variant	rs1519551
Chromosome Location	chr4:142570472-142570473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12508866	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs13117878	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13126364	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2030326	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2090664	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2139383	0.82[AFR][1000 genomes]
rs55849760	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs932209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[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	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1519551	IL15	cis	multi-tissue	Pritchard
rs1519551	INPP4B	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142559800-142574000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:142560000-142575200	Weak transcription	Right Atrium	heart
3	chr4:142564000-142575200	Weak transcription	Psoas Muscle	Psoas
4	chr4:142565400-142580600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:142566200-142573400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:142567800-142573200	Weak transcription	NH-A	brain
7	chr4:142567800-142586400	Weak transcription	HSMM	muscle
8	chr4:142568600-142573000	Weak transcription	Fetal Heart	heart
9	chr4:142568600-142573400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:142568800-142581000	Weak transcription	A549	lung
11	chr4:142569200-142573400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:142569200-142573400	Weak transcription	Osteobl	bone
13	chr4:142569200-142575200	Weak transcription	Aorta	Aorta
14	chr4:142569200-142577000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:142569200-142582800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:142569400-142573200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:142569400-142573400	Weak transcription	Small Intestine	intestine
18	chr4:142569400-142573800	Weak transcription	NHLF	lung
19	chr4:142570000-142570600	Enhancers	Adipose Nuclei	Adipose
20	chr4:142570000-142570600	Enhancers	Liver	Liver
21	chr4:142570200-142570600	Enhancers	Stomach Smooth Muscle	stomach
22	chr4:142570200-142570800	ZNF genes & repeats	GM12878-XiMat	blood
23	chr4:142570200-142573200	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:142570200-142573400	Weak transcription	NHDF-Ad	bronchial
25	chr4:142570200-142579200	Weak transcription	Spleen	Spleen
26	chr4:142570400-142573000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:142570400-142586400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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