Variant report

Variant	rs17669146
Chromosome Location	chr3:61552092-61552093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1574016	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1878772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2886519	0.80[ASN][1000 genomes]
rs4688636	0.86[CHB][hapmap]
rs6445222	0.95[ASN][1000 genomes]
rs6445224	0.97[ASN][1000 genomes]
rs7636186	0.95[ASN][1000 genomes]
rs7640434	0.86[CHB][hapmap]
rs9808938	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9821236	0.88[ASN][1000 genomes]
rs9824541	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9827952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9840322	0.95[ASN][1000 genomes]
rs9845678	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17669146	ABHD6	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61549800-61553000	Weak transcription	Small Intestine	intestine
2	chr3:61550200-61552600	Enhancers	HepG2	liver
3	chr3:61550400-61554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:61550600-61552200	Weak transcription	Lung	lung
5	chr3:61550600-61568600	Weak transcription	Pancreas	Pancrea
6	chr3:61550800-61552200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:61550800-61552400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:61550800-61552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:61550800-61555400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:61550800-61556800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:61550800-61556800	Weak transcription	Ovary	ovary
12	chr3:61550800-61557600	Weak transcription	Psoas Muscle	Psoas
13	chr3:61550800-61558400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:61550800-61574200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:61551000-61552200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:61551000-61552200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:61551000-61552200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:61551000-61552200	Enhancers	Colon Smooth Muscle	Colon
19	chr3:61551000-61552200	Enhancers	NHDF-Ad	bronchial
20	chr3:61551000-61552400	Weak transcription	Liver	Liver
21	chr3:61551000-61552600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:61551000-61552800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:61551000-61552800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr3:61551000-61554800	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:61551000-61555800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:61551000-61556800	Weak transcription	NH-A	brain
27	chr3:61551000-61557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:61551000-61557600	Weak transcription	Aorta	Aorta
29	chr3:61551000-61557600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:61551000-61557600	Weak transcription	Right Atrium	heart
31	chr3:61551000-61559800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:61551000-61559800	Weak transcription	NHEK	skin
33	chr3:61551000-61561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:61551200-61552200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:61551200-61552400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:61551200-61555600	Weak transcription	Fetal Lung	lung
37	chr3:61551200-61555800	Weak transcription	Brain Anterior Caudate	brain
38	chr3:61551200-61556400	Weak transcription	Fetal Brain Male	brain
39	chr3:61551200-61557600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:61551200-61560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:61551400-61555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:61551400-61555800	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:61551600-61552200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:61551600-61553000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:61551600-61554800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:61551600-61554800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:61551600-61555400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:61551600-61556800	Weak transcription	Right Ventricle	heart
49	chr3:61551600-61557600	Weak transcription	Fetal Kidney	kidney
50	chr3:61551600-61559800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links