Variant report

Variant	rs66688787
Chromosome Location	chr17:15686884-15686885
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11078315	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939797	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34071462	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508959	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv907705	chr17:15611495-15717546	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv11477	chr17:15676903-15688164	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
11	nsv442411	chr17:15677001-15694785	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs66688787	CTD-3157E16.1	cis	Thyroid	GTEx
rs66688787	MEIS3P1	cis	Artery Tibial	GTEx
rs66688787	CTD-3157E16.1	cis	Adipose Subcutaneous	GTEx
rs66688787	CTD-3157E16.1	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15685600-15687200	Enhancers	Colon Smooth Muscle	Colon
2	chr17:15686400-15689400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:15686400-15689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:15686600-15687000	Enhancers	Duodenum Mucosa	Duodenum
5	chr17:15686600-15687600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:15686600-15687600	Weak transcription	Fetal Stomach	stomach
7	chr17:15686600-15687600	Weak transcription	Right Atrium	heart
8	chr17:15686600-15688200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr17:15686600-15688400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:15686600-15688600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:15686600-15688600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:15686600-15688800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr17:15686600-15689000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:15686600-15689000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:15686600-15689200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:15686600-15689200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:15686600-15689200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:15686600-15689200	Weak transcription	Fetal Brain Female	brain
19	chr17:15686600-15689200	Weak transcription	Ovary	ovary
20	chr17:15686600-15689200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr17:15686600-15689200	Weak transcription	Right Ventricle	heart
22	chr17:15686600-15689200	Weak transcription	HSMM	muscle
23	chr17:15686600-15689200	Weak transcription	NHLF	lung
24	chr17:15686600-15689400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr17:15686600-15689400	Weak transcription	Aorta	Aorta
26	chr17:15686600-15689400	Weak transcription	Colonic Mucosa	Colon
27	chr17:15686600-15689400	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:15686600-15689400	Weak transcription	Left Ventricle	heart
29	chr17:15686600-15689400	Weak transcription	HMEC	breast
30	chr17:15686600-15689600	Weak transcription	Brain Germinal Matrix	brain
31	chr17:15686600-15689600	Weak transcription	Esophagus	oesophagus
32	chr17:15686600-15689600	Weak transcription	Lung	lung
33	chr17:15686600-15689600	Weak transcription	Pancreas	Pancrea
34	chr17:15686600-15689600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:15686600-15689600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr17:15686600-15689600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr17:15686600-15689800	Weak transcription	Placenta	Placenta
38	chr17:15686600-15690600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:15686600-15691400	Weak transcription	Gastric	stomach
40	chr17:15686800-15687000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:15686800-15687600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:15686800-15688200	Enhancers	Fetal Lung	lung
43	chr17:15686800-15689000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:15686800-15689000	Weak transcription	Adipose Nuclei	Adipose
45	chr17:15686800-15689200	Weak transcription	Osteobl	bone
46	chr17:15686800-15689400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links