Variant report

Variant	rs8054696
Chromosome Location	chr16:48492861-48492862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004704	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs11076569	0.80[ASN][1000 genomes]
rs11643514	0.88[ASN][1000 genomes]
rs11644887	0.95[ASN][1000 genomes]
rs11648225	0.82[ASN][1000 genomes]
rs11865776	0.91[ASN][1000 genomes]
rs1566466	0.88[ASN][1000 genomes]
rs1566467	0.88[ASN][1000 genomes]
rs2062553	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2062554	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2088753	0.88[ASN][1000 genomes]
rs2088754	0.88[ASN][1000 genomes]
rs4785244	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4785520	0.88[ASN][1000 genomes]
rs4785521	0.80[ASN][1000 genomes]
rs55745119	0.85[ASN][1000 genomes]
rs56207849	0.95[ASN][1000 genomes]
rs7184700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs7194822	0.83[ASN][1000 genomes]
rs7198215	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198420	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7203475	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206781	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8046716	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs8052026	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs8056201	0.82[ASN][1000 genomes]
rs8056346	0.82[ASN][1000 genomes]
rs8063059	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9888862	0.91[ASN][1000 genomes]
rs9889065	0.91[ASN][1000 genomes]
rs9889067	0.91[ASN][1000 genomes]
rs9921402	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9923092	0.88[ASN][1000 genomes]
rs9926683	0.88[ASN][1000 genomes]
rs9933892	0.82[ASN][1000 genomes]
rs9939368	0.85[ASN][1000 genomes]
rs9940599	0.88[ASN][1000 genomes]
rs9941289	0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8054696	PAPD5	cis	cerebellum	SCAN
rs8054696	NOD2	cis	cerebellum	SCAN
rs8054696	NKD1	cis	cerebellum	SCAN
rs8054696	SNX20	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48488200-48495400	Enhancers	Primary B cells from peripheral blood	blood
2	chr16:48489400-48493000	Weak transcription	Primary B cells from cord blood	blood
3	chr16:48490800-48493200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:48491200-48493400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr16:48491400-48493000	Enhancers	Hela-S3	cervix
6	chr16:48491400-48493200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:48491600-48493200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:48491600-48493200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr16:48491600-48493400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:48491600-48493400	Enhancers	HMEC	breast
11	chr16:48491600-48493800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:48491800-48493200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:48491800-48493400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:48492000-48493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:48492000-48493000	Enhancers	Osteobl	bone
16	chr16:48492000-48493200	Enhancers	Stomach Mucosa	stomach
17	chr16:48492000-48493400	Enhancers	NH-A	brain
18	chr16:48492400-48493000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr16:48492400-48493200	Enhancers	A549	lung
20	chr16:48492400-48493800	Enhancers	NHEK	skin
21	chr16:48492600-48493000	Flanking Active TSS	GM12878-XiMat	blood
22	chr16:48492600-48493200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:48492600-48493200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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