Variant report

Variant	rs1156545
Chromosome Location	chr8:120080692-120080693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNFRSF11B-1	chr8:120079913-120081021	ENSG00000254278.1

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1351954	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1385492	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1385493	0.89[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs1385496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1385497	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385498	0.92[CEU][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1485298	0.91[YRI][hapmap]
rs1872424	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2242313	0.92[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2247769	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450058	0.91[YRI][hapmap]
rs2450072	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2450076	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2450080	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465385	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs2465390	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2465393	0.83[EUR][1000 genomes]
rs2465395	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6469811	0.81[EUR][1000 genomes]
rs7813952	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs996789	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1156545	NOV	cis	cerebellum	SCAN
rs1156545	SAMD12	cis	parietal	SCAN
rs1156545	MAL2	cis	cerebellum	SCAN
rs1156545	TNFRSF11B	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120079400-120081000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
2	chr8:120079800-120080800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:120079800-120081000	Enhancers	Adipose Nuclei	Adipose
4	chr8:120080000-120082400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr8:120080000-120082600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:120080600-120081200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:120080600-120082000	Weak transcription	Hela-S3	cervix
8	chr8:120080600-120082200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:120080600-120083400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:120080600-120085200	Weak transcription	Fetal Stomach	stomach

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