Variant report

Variant	rs17290109
Chromosome Location	chr9:14746846-14746847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10961658	1.00[YRI][hapmap]
rs11789504	0.82[CEU][hapmap];0.97[AMR][1000 genomes]
rs11794846	1.00[YRI][hapmap]
rs12115314	1.00[YRI][hapmap]
rs12115487	1.00[YRI][hapmap]
rs17218977	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs2131883	1.00[YRI][hapmap]
rs41265300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4297129	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4412445	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4579619	0.88[AMR][1000 genomes]
rs4606156	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7033371	0.80[AMR][1000 genomes]
rs7036802	0.80[AMR][1000 genomes]
rs7047712	1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes]
rs73413719	0.97[EUR][1000 genomes]
rs7858241	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs954118	0.85[MEX][hapmap]

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	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
4	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv933345	chr9:14695436-14750474	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv892614	chr9:14712257-14756969	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv934201	chr9:14740238-14748544	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17290109	CER1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14730800-14764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:14732600-14755200	Weak transcription	Fetal Intestine Large	intestine
3	chr9:14733600-14749000	Strong transcription	HepG2	liver
4	chr9:14740400-14749600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:14741600-14750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:14743600-14749600	Weak transcription	Fetal Heart	heart
7	chr9:14744800-14747800	Strong transcription	Fetal Muscle Leg	muscle
8	chr9:14744800-14748800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:14744800-14748800	Strong transcription	Adipose Nuclei	Adipose
10	chr9:14745000-14751800	Strong transcription	Fetal Kidney	kidney
11	chr9:14745000-14809800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:14745400-14748000	Enhancers	HUVEC	blood vessel
13	chr9:14745400-14748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:14745400-14749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:14745400-14751400	Strong transcription	Fetal Lung	lung
16	chr9:14745600-14748200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:14745600-14749400	Strong transcription	Colon Smooth Muscle	Colon
18	chr9:14745800-14748800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr9:14745800-14752400	Weak transcription	Fetal Intestine Small	intestine
20	chr9:14746000-14748800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:14746200-14747000	Strong transcription	Fetal Stomach	stomach
22	chr9:14746200-14747200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:14746200-14747200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr9:14746200-14747400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:14746200-14748200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:14746200-14749000	Strong transcription	Pancreas	Pancrea
27	chr9:14746200-14749200	Strong transcription	Aorta	Aorta
28	chr9:14746400-14747200	Enhancers	NHEK	skin
29	chr9:14746400-14747400	Enhancers	HMEC	breast
30	chr9:14746400-14748800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:14746600-14747200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:14746800-14747000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:14746800-14747200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr9:14746800-14747400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr9:14746800-14747400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links