Variant report

Variant	rs16952722
Chromosome Location	chr18:7963085-7963086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10153443	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12326176	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12326185	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12954431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12956961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12957388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12957993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12959314	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12960276	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12963759	0.88[EUR][1000 genomes]
rs12966777	0.96[EUR][1000 genomes]
rs12968232	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13381485	0.82[EUR][1000 genomes]
rs16952586	1.00[CHB][hapmap]
rs16952705	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28434244	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34017251	0.95[EUR][1000 genomes]
rs34046553	0.95[EUR][1000 genomes]
rs34049036	0.95[EUR][1000 genomes]
rs34296167	0.95[EUR][1000 genomes]
rs34554615	0.94[EUR][1000 genomes]
rs34580701	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35308699	0.95[EUR][1000 genomes]
rs35521625	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35558945	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35822807	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35830277	0.83[EUR][1000 genomes]
rs36093720	0.82[EUR][1000 genomes]
rs7239786	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7240582	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs8087770	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs8087884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8089133	0.95[EUR][1000 genomes]
rs8092781	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9807495	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952741	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs9956981	0.82[EUR][1000 genomes]
rs9961079	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9966320	1.00[CHB][hapmap]

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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv521059	chr18:7962217-7981018	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16952722	NAPG	cis	parietal	SCAN
rs16952722	BOK	trans	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr18:7947200-7981400	Weak transcription	Fetal Stomach	stomach
3	chr18:7947400-7963400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:7947400-7963600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:7947400-7965600	Weak transcription	Thymus	Thymus
6	chr18:7947800-7967600	Weak transcription	Primary T cells from cord blood	blood
7	chr18:7948000-7965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr18:7948000-7967200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:7948000-7975000	Weak transcription	Pancreas	Pancrea
10	chr18:7951200-7963400	Weak transcription	Adipose Nuclei	Adipose
11	chr18:7951600-7965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:7954400-7966000	Weak transcription	Fetal Kidney	kidney
13	chr18:7955400-7965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:7955600-7963400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr18:7956000-7965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:7956000-7966200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:7956000-7980800	Weak transcription	Fetal Thymus	thymus
18	chr18:7956000-7982400	Weak transcription	Fetal Muscle Leg	muscle
19	chr18:7957600-7965200	Weak transcription	Lung	lung
20	chr18:7957600-7980600	Weak transcription	Right Ventricle	heart
21	chr18:7958600-7963200	Weak transcription	Brain Anterior Caudate	brain
22	chr18:7958800-7963400	Weak transcription	Aorta	Aorta
23	chr18:7959000-7963200	Weak transcription	Right Atrium	heart
24	chr18:7959000-7963600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr18:7959000-7963800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr18:7959000-7964200	Weak transcription	NHDF-Ad	bronchial
27	chr18:7959000-7987400	Weak transcription	Ovary	ovary
28	chr18:7959200-7963800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:7959200-7963800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:7959200-7982400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:7959600-7963600	Weak transcription	Osteobl	bone
32	chr18:7959600-7963800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:7959600-7963800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr18:7959800-7963200	Weak transcription	Small Intestine	intestine
35	chr18:7959800-7965400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:7959800-7967800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr18:7960000-7964200	Weak transcription	Hela-S3	cervix
38	chr18:7960800-7967000	Weak transcription	Fetal Lung	lung
39	chr18:7961200-7964800	Enhancers	A549	lung
40	chr18:7961600-7963800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr18:7962400-7963600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:7962400-7964000	Enhancers	Psoas Muscle	Psoas
43	chr18:7962600-7963600	Enhancers	Left Ventricle	heart
44	chr18:7962600-7974000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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