Variant report

Variant	rs3019286
Chromosome Location	chr8:99895405-99895406
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	chr8:99894098..99895893-chr8:99922111..99925034,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPAL2-5	chr8:99891126-99896062	NONHSAT127935

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10447977	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs11778767	0.91[CHB][hapmap]
rs11780500	0.91[CHB][hapmap]
rs12114834	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs12541317	0.90[CHB][hapmap]
rs12679734	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs13269932	0.83[MEX][hapmap]
rs13275915	0.83[MEX][hapmap]
rs1447245	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1476181	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1961744	0.80[ASN][1000 genomes]
rs2442015	0.89[YRI][hapmap]
rs2515214	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2515216	0.84[TSI][hapmap]
rs2515219	0.84[YRI][hapmap]
rs2922066	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2922068	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs2922075	0.81[ASN][1000 genomes]
rs2922076	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2922078	0.95[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs2922081	0.81[ASN][1000 genomes]
rs2922082	0.93[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2922084	0.99[ASN][1000 genomes]
rs3019290	0.88[ASN][1000 genomes]
rs3019291	0.87[ASN][1000 genomes]
rs34366206	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs35798019	0.91[CHB][hapmap];0.82[TSI][hapmap]
rs4131873	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4255105	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs4279561	0.83[MEX][hapmap]
rs4292660	0.91[JPT][hapmap]
rs4413739	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4549741	0.83[MEX][hapmap]
rs4562286	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4734417	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4735574	0.83[MEX][hapmap]
rs7827435	0.91[JPT][hapmap]
rs7838239	0.91[CHB][hapmap]
rs7845271	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3019286	OSR2	cis	cerebellum	SCAN
rs3019286	FBXO43	cis	parietal	SCAN
rs3019286	STK3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99878400-99896000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:99889000-99898000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:99889600-99900000	Weak transcription	Ovary	ovary
4	chr8:99894800-99895800	Weak transcription	Placenta	Placenta
5	chr8:99894800-99896600	Enhancers	HMEC	breast
6	chr8:99894800-99897400	Enhancers	NHEK	skin
7	chr8:99894800-99897600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:99895000-99896400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:99895000-99896600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:99895200-99895800	Enhancers	Osteobl	bone
11	chr8:99895200-99896000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:99895200-99896000	Enhancers	Fetal Muscle Leg	muscle
13	chr8:99895200-99896000	Enhancers	NHDF-Ad	bronchial
14	chr8:99895200-99896200	Enhancers	Fetal Stomach	stomach
15	chr8:99895400-99895800	Enhancers	A549	lung
16	chr8:99895400-99896200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:99895400-99896200	Enhancers	Hela-S3	cervix
18	chr8:99895400-99896800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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