Variant report

Variant	rs565293
Chromosome Location	chr9:97923592-97923593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1045276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10491560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10761376	0.81[EUR][1000 genomes]
rs10761381	0.83[CHB][hapmap]
rs10821450	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs171417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs187172	1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs2282216	0.85[JPT][hapmap]
rs2404692	0.83[TSI][hapmap]
rs356666	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs356669	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs356673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356677	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs356678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs356679	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs356680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356683	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356687	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs356688	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs356689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3780567	0.90[JPT][hapmap]
rs3824486	0.85[JPT][hapmap]
rs416792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs437511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647376	0.95[JPT][hapmap]
rs4647534	0.90[JPT][hapmap]
rs4744451	0.90[JPT][hapmap]
rs526189	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs540412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609324	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs657637	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7033633	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs7863582	0.81[EUR][1000 genomes]
rs7865753	0.81[EUR][1000 genomes]
rs944934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
2	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs565293	TDRD7	cis	cerebellum	SCAN
rs565293	PHF2	cis	cerebellum	SCAN
rs565293	NINJ1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
3	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:97900800-97930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:97901600-97925000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:97902000-97929800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:97905800-97924000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:97906400-97933000	Weak transcription	Fetal Kidney	kidney
9	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:97910800-97933000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:97911200-97930000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:97913200-97929000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:97913200-97930200	Weak transcription	Primary T cells from cord blood	blood
14	chr9:97913400-97929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:97917400-97925200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:97920000-97925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
18	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
19	chr9:97920400-97925600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:97920400-97930400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:97920400-97951800	Weak transcription	HepG2	liver
22	chr9:97920600-97925200	Weak transcription	Adipose Nuclei	Adipose
23	chr9:97920600-97925200	Weak transcription	Psoas Muscle	Psoas
24	chr9:97920600-97925800	Weak transcription	Fetal Stomach	stomach
25	chr9:97920600-97930400	Weak transcription	Liver	Liver
26	chr9:97920600-97931000	Weak transcription	Fetal Lung	lung
27	chr9:97920600-97933000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:97920600-97933400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:97920800-97931400	Weak transcription	Hela-S3	cervix
30	chr9:97920800-97931400	Weak transcription	K562	blood
31	chr9:97920800-97932800	Weak transcription	GM12878-XiMat	blood
32	chr9:97921200-97930400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:97923400-97923600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr9:97923400-97923800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:97923400-97923800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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