Variant report

Variant	rs12716948
Chromosome Location	chr16:82678897-82678898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11861857	0.93[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3844415	0.89[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs3910223	0.88[AFR][1000 genomes]
rs3910226	0.90[AFR][1000 genomes]
rs3910228	0.88[AFR][1000 genomes]
rs3910229	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs6565052	0.82[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6565053	0.95[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs7184391	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7185267	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs9924250	1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532598	chr16:82034475-82738733	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1065896	chr16:82213517-82731994	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv833305	chr16:82563888-82722084	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059718	chr16:82564054-82810003	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12716948	BCMO1	cis	cerebellum	SCAN
rs12716948	FAM92B	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82672000-82679200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:82672000-82681400	Weak transcription	Esophagus	oesophagus
3	chr16:82672200-82685800	Weak transcription	HSMMtube	muscle
4	chr16:82673800-82685600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr16:82674800-82679000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:82675000-82679400	Enhancers	Fetal Heart	heart
7	chr16:82675400-82682800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:82675400-82682800	Weak transcription	HMEC	breast
9	chr16:82675600-82680600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:82675600-82680600	Weak transcription	Right Ventricle	heart
11	chr16:82675600-82682400	Weak transcription	HSMM	muscle
12	chr16:82675600-82683000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr16:82676400-82680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr16:82676600-82679000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr16:82676600-82679200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr16:82676800-82681000	Weak transcription	Colonic Mucosa	Colon
17	chr16:82677000-82679800	Weak transcription	Psoas Muscle	Psoas
18	chr16:82677200-82679200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr16:82677200-82679800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:82677200-82683800	Weak transcription	GM12878-XiMat	blood
21	chr16:82678000-82679000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr16:82678000-82679200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:82678000-82685600	Weak transcription	Fetal Muscle Leg	muscle
24	chr16:82678000-82687000	Weak transcription	Lung	lung
25	chr16:82678200-82679000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:82678200-82679200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:82678200-82679600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr16:82678200-82682600	Weak transcription	NHEK	skin
29	chr16:82678400-82679000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr16:82678400-82679400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr16:82678400-82679600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr16:82678400-82683200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:82678400-82687000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:82678600-82679400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr16:82678800-82679000	Enhancers	Osteobl	bone
36	chr16:82678800-82679200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr16:82678800-82679200	Enhancers	Left Ventricle	heart
38	chr16:82678800-82679400	Enhancers	NH-A	brain

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