Variant report

Variant	rs11659625
Chromosome Location	chr18:9479989-9479990
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10468797	0.94[CEU][hapmap];0.83[CHB][hapmap]
rs11664312	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12454987	0.94[CEU][hapmap];0.83[CHB][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs12457094	0.87[CHB][hapmap]
rs16955157	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs1813100	0.87[CHB][hapmap]
rs2061692	0.88[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs329026	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs329027	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs329028	0.91[CHB][hapmap]
rs4798816	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57491759	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58103465	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58651706	0.85[EUR][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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11659625	RAB31	cis	parietal	SCAN
rs11659625	MPPE1	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9476600-9481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:9476600-9481800	Weak transcription	Pancreas	Pancrea
3	chr18:9476600-9484200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:9476800-9480400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr18:9476800-9481200	Weak transcription	Right Atrium	heart
6	chr18:9476800-9482400	Weak transcription	Brain Anterior Caudate	brain
7	chr18:9476800-9494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr18:9476800-9496000	Weak transcription	Stomach Mucosa	stomach
9	chr18:9477000-9480000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr18:9477000-9481400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr18:9477000-9482400	Weak transcription	Primary T cells from cord blood	blood
12	chr18:9477000-9482400	Weak transcription	Right Ventricle	heart
13	chr18:9477000-9482800	Weak transcription	Brain Hippocampus Middle	brain
14	chr18:9477000-9483600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr18:9477000-9485400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr18:9477000-9486000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr18:9477000-9489800	Weak transcription	HUVEC	blood vessel
18	chr18:9477000-9514000	Weak transcription	NH-A	brain
19	chr18:9477200-9481800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr18:9477200-9482000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:9477200-9482000	Weak transcription	Osteobl	bone
22	chr18:9477200-9482400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr18:9477200-9482400	Weak transcription	Psoas Muscle	Psoas
24	chr18:9477200-9482400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr18:9477200-9484200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr18:9477200-9513800	Weak transcription	HSMM	muscle
27	chr18:9477400-9482400	Weak transcription	Adipose Nuclei	Adipose
28	chr18:9477400-9482400	Weak transcription	Brain Substantia Nigra	brain
29	chr18:9477400-9485000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr18:9477400-9492400	Weak transcription	A549	lung
31	chr18:9477400-9493600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr18:9477600-9482400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr18:9477600-9482800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr18:9477600-9484000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr18:9477600-9484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr18:9477600-9485000	Weak transcription	Liver	Liver
37	chr18:9477600-9485200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr18:9477600-9488000	Weak transcription	HepG2	liver
39	chr18:9477600-9491000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr18:9477600-9494400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr18:9477800-9481800	Weak transcription	Colon Smooth Muscle	Colon
42	chr18:9477800-9482400	Weak transcription	Brain Angular Gyrus	brain
43	chr18:9477800-9482600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr18:9477800-9484000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr18:9477800-9488600	Weak transcription	Fetal Lung	lung
46	chr18:9477800-9494800	Weak transcription	HMEC	breast
47	chr18:9477800-9501800	Weak transcription	NHDF-Ad	bronchial
48	chr18:9477800-9503200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr18:9478000-9480200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr18:9478000-9480600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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