Variant report

Variant	rs9899355
Chromosome Location	chr17:17898243-17898244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11078408	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11650021	0.85[EUR][1000 genomes]
rs11869491	0.97[EUR][1000 genomes]
rs11870660	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11871231	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12150369	0.93[EUR][1000 genomes]
rs12939020	0.84[EUR][1000 genomes]
rs28537385	0.94[EUR][1000 genomes]
rs2955350	0.87[EUR][1000 genomes]
rs2955353	0.87[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955359	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955368	0.86[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2955377	0.90[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2955378	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2955380	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955381	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955384	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2955385	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2974999	0.89[CEU][hapmap]
rs4072738	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072739	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4299203	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4365348	0.93[EUR][1000 genomes]
rs4368210	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4426402	0.89[CEU][hapmap]
rs4459604	0.95[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4471742	0.80[EUR][1000 genomes]
rs4506969	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs4643387	0.84[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs4925119	0.81[YRI][hapmap]
rs4925133	0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4925135	0.87[EUR][1000 genomes]
rs4925136	0.86[EUR][1000 genomes]
rs4925137	0.86[JPT][hapmap]
rs57728924	0.80[EUR][1000 genomes]
rs62072048	0.86[EUR][1000 genomes]
rs62072050	0.92[EUR][1000 genomes]
rs6502631	0.93[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs6502633	0.89[EUR][1000 genomes]
rs6502634	0.83[EUR][1000 genomes]
rs6502636	0.94[CEU][hapmap]
rs7207461	0.87[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7209003	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7210400	0.87[EUR][1000 genomes]
rs7211714	0.89[CEU][hapmap]
rs7212167	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs7212447	0.89[CEU][hapmap]
rs7215524	0.92[EUR][1000 genomes]
rs721669	0.89[CEU][hapmap]
rs7219320	0.80[MEX][hapmap];0.93[TSI][hapmap]
rs7219324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223696	0.92[EUR][1000 genomes]
rs7224047	0.91[EUR][1000 genomes]
rs7406982	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7503738	0.87[EUR][1000 genomes]
rs8068175	0.85[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs8069811	0.92[EUR][1000 genomes]
rs8071238	0.86[EUR][1000 genomes]
rs8075189	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs8080602	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs8082590	0.80[EUR][1000 genomes]
rs854763	0.89[CEU][hapmap]
rs854767	0.89[CEU][hapmap]
rs854769	0.89[CEU][hapmap]
rs854790	0.89[CEU][hapmap]
rs854791	0.89[CEU][hapmap]
rs854809	0.89[CEU][hapmap]
rs854814	0.89[CEU][hapmap]
rs854817	0.89[CEU][hapmap]
rs9303144	0.89[CEU][hapmap]
rs9894138	0.87[EUR][1000 genomes]
rs9896837	0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs9897761	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs9911850	0.93[EUR][1000 genomes]
rs9912096	0.94[EUR][1000 genomes]
rs9913277	0.95[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9914127	0.81[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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS 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 miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9899355	TOM1L2	cis	parietal	SCAN
rs9899355	TOM1L2	cis	cerebellum	SCAN
rs9899355	C17orf39	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17903200	Weak transcription	Gastric	stomach
2	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
3	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
4	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:17877000-17900000	Weak transcription	Fetal Intestine Small	intestine
6	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
7	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
9	chr17:17887200-17900800	Weak transcription	Left Ventricle	heart
10	chr17:17889000-17907400	Weak transcription	Brain Anterior Caudate	brain
11	chr17:17890000-17907400	Weak transcription	Brain Germinal Matrix	brain
12	chr17:17892200-17908400	Weak transcription	Lung	lung
13	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
15	chr17:17892800-17908000	Weak transcription	Spleen	Spleen
16	chr17:17893600-17900000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:17894000-17903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
19	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:17895000-17898600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:17895000-17903400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:17895200-17909600	Weak transcription	NHLF	lung
23	chr17:17896800-17898400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:17896800-17898600	Enhancers	HSMMtube	muscle
25	chr17:17896800-17898800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:17896800-17899000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr17:17897000-17898400	Enhancers	Fetal Muscle Leg	muscle
28	chr17:17897000-17898600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:17897000-17898600	Enhancers	Esophagus	oesophagus
30	chr17:17897200-17898600	Enhancers	Placenta	Placenta
31	chr17:17897200-17899200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:17897400-17898400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:17897400-17898800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:17897400-17898800	Enhancers	Fetal Heart	heart
35	chr17:17897600-17898400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr17:17897600-17898600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:17897600-17898600	Enhancers	Ovary	ovary
38	chr17:17897600-17898800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr17:17897800-17898400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:17897800-17898400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:17897800-17898400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:17897800-17898400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:17897800-17898400	Enhancers	Fetal Thymus	thymus
44	chr17:17897800-17898400	Enhancers	NHDF-Ad	bronchial
45	chr17:17897800-17898600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:17897800-17898600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr17:17897800-17898600	Enhancers	Adipose Nuclei	Adipose
48	chr17:17897800-17898600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr17:17897800-17898800	Genic enhancers	Fetal Stomach	stomach
50	chr17:17897800-17898800	Enhancers	NHEK	skin

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