Variant report

Variant	rs3916255
Chromosome Location	chr16:12093755-12093756
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr16:12093678-12093802	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SNX29	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10163386	0.97[ASN][1000 genomes]
rs11075041	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11639821	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11641950	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11644227	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11648938	0.84[AMR][1000 genomes]
rs11859213	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11862467	0.83[AMR][1000 genomes]
rs13334063	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844112	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59446863	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6498260	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6498261	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6498262	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7197059	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7206768	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8044943	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8051012	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8060439	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9929844	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	nsv984259	chr16:12092609-12104575	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3916255	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:81 , 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	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
4	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:12072400-12096400	Weak transcription	Ovary	ovary
7	chr16:12072400-12104400	Weak transcription	NHLF	lung
8	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:12079600-12109600	Weak transcription	Gastric	stomach
13	chr16:12080200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:12083400-12102800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
16	chr16:12086800-12096600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:12088200-12100800	Weak transcription	Fetal Brain Female	brain
18	chr16:12088600-12093800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:12088600-12098200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr16:12088600-12104200	Weak transcription	Right Ventricle	heart
21	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
22	chr16:12088600-12110000	Weak transcription	NH-A	brain
23	chr16:12088800-12094400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr16:12088800-12096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:12088800-12096400	Weak transcription	Right Atrium	heart
26	chr16:12088800-12098600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr16:12088800-12106600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr16:12088800-12108200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr16:12088800-12115400	Weak transcription	Placenta	Placenta
30	chr16:12089000-12093800	Weak transcription	Brain Anterior Caudate	brain
31	chr16:12089000-12093800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr16:12089000-12093800	Weak transcription	Lung	lung
33	chr16:12089000-12094000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:12089000-12094400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:12089000-12094400	Weak transcription	Left Ventricle	heart
36	chr16:12089000-12094600	Weak transcription	Brain Angular Gyrus	brain
37	chr16:12089000-12099800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:12089000-12104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:12089400-12103000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:12090200-12094200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:12090800-12093800	Weak transcription	Aorta	Aorta
42	chr16:12090800-12093800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:12090800-12096400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr16:12091000-12093800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:12091000-12103000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:12091200-12093800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr16:12091200-12095600	Weak transcription	K562	blood
48	chr16:12091200-12096400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:12091200-12096400	Weak transcription	Fetal Muscle Leg	muscle
50	chr16:12091200-12096600	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links