Variant report

Variant	rs11862467
Chromosome Location	chr16:12108545-12108546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11075041	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639821	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11641950	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644227	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11859213	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13334063	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34701893	0.83[AFR][1000 genomes]
rs3844112	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3916255	0.83[AMR][1000 genomes]
rs55995758	0.82[EUR][1000 genomes]
rs59446863	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62037701	0.91[ASN][1000 genomes]
rs6498260	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6498261	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6498262	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7197059	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7206768	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8044943	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051012	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051349	0.80[AMR][1000 genomes]
rs8060439	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9929844	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3360290	chr16:12106276-12108824	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
7	esv3394654	chr16:12106501-12108749	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11862467	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12079600-12109600	Weak transcription	Gastric	stomach
4	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
5	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
6	chr16:12088600-12110000	Weak transcription	NH-A	brain
7	chr16:12088800-12115400	Weak transcription	Placenta	Placenta
8	chr16:12092400-12110200	Weak transcription	NHEK	skin
9	chr16:12094200-12110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:12096800-12110000	Weak transcription	Osteobl	bone
11	chr16:12096800-12111800	Weak transcription	Ovary	ovary
12	chr16:12097000-12109400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:12097600-12110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
15	chr16:12098600-12109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:12098600-12118200	Weak transcription	Pancreas	Pancrea
17	chr16:12099000-12109400	Weak transcription	Brain Germinal Matrix	brain
18	chr16:12099400-12118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr16:12099600-12111800	Weak transcription	Fetal Muscle Leg	muscle
20	chr16:12099600-12112600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr16:12101400-12110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr16:12101800-12110000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:12101800-12111600	Weak transcription	HSMMtube	muscle
26	chr16:12101800-12121400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr16:12101800-12123600	Weak transcription	Lung	lung
28	chr16:12101800-12129800	Weak transcription	Aorta	Aorta
29	chr16:12102000-12124200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:12104200-12111600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr16:12104400-12109800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:12104600-12109400	Weak transcription	Left Ventricle	heart
33	chr16:12104600-12110600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:12104600-12116400	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:12104800-12110200	Weak transcription	NHLF	lung
36	chr16:12105000-12109800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr16:12105000-12110200	Weak transcription	GM12878-XiMat	blood
38	chr16:12105000-12120600	Weak transcription	Brain Substantia Nigra	brain
39	chr16:12105200-12110200	Weak transcription	NHDF-Ad	bronchial
40	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr16:12105400-12120800	Weak transcription	Fetal Thymus	thymus
42	chr16:12105600-12110400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:12105800-12110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:12105800-12115800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr16:12105800-12120800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr16:12105800-12124200	Weak transcription	Primary T cells from cord blood	blood
47	chr16:12106000-12111000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:12106200-12114800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr16:12106400-12109600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:12106800-12110400	Weak transcription	Primary B cells from cord blood	blood

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