Variant report

Variant	rs11089599
Chromosome Location	chr22:33363999-33364000
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10483168	1.00[JPT][hapmap]
rs11703516	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703670	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703817	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703888	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704480	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704652	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11704744	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704887	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704993	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12157614	1.00[YRI][hapmap]
rs12157696	1.00[YRI][hapmap]
rs12158631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12160160	1.00[YRI][hapmap]
rs133928	1.00[CHB][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap]
rs137543	1.00[CHB][hapmap]
rs137559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137560	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137564	0.87[AMR][1000 genomes]
rs17779789	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042793	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35463351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441575	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994648	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994649	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5994654	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5998660	1.00[YRI][hapmap]
rs5998668	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998671	1.00[YRI][hapmap]
rs5998677	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998681	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998682	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998685	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998689	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5998693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5998697	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73158385	0.82[AMR][1000 genomes]
rs73158393	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73162010	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162024	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162026	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162029	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162032	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139118	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139584	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142585	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11089599	MYO1E	trans	parietal	SCAN
rs11089599	MTMR3	cis	parietal	SCAN
rs11089599	GAL3ST1	cis	cerebellum	SCAN
rs11089599	C22orf27	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33314000-33380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:33343200-33372600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr22:33348000-33382400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:33354000-33374000	Weak transcription	Brain Angular Gyrus	brain
5	chr22:33354400-33381800	Weak transcription	Fetal Brain Male	brain
6	chr22:33354600-33387400	Weak transcription	Fetal Brain Female	brain
7	chr22:33361000-33371400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr22:33361000-33380400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr22:33361200-33368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:33362200-33364400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr22:33362200-33365800	Enhancers	Duodenum Mucosa	Duodenum
12	chr22:33362200-33365800	Enhancers	Fetal Intestine Small	intestine
13	chr22:33362200-33366400	Enhancers	Fetal Intestine Large	intestine
14	chr22:33362400-33365800	Enhancers	Liver	Liver
15	chr22:33362800-33364600	Enhancers	Fetal Kidney	kidney
16	chr22:33363000-33364000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr22:33363000-33364200	Enhancers	Rectal Smooth Muscle	rectum
18	chr22:33363000-33364400	Enhancers	Fetal Lung	lung
19	chr22:33363000-33364800	Enhancers	Fetal Stomach	stomach
20	chr22:33363200-33364000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr22:33363200-33364000	Flanking Active TSS	HepG2	liver
22	chr22:33363200-33364800	Enhancers	Stomach Smooth Muscle	stomach
23	chr22:33363200-33365800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr22:33363400-33364000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr22:33363400-33364600	Enhancers	Colon Smooth Muscle	Colon
26	chr22:33363400-33365800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:33363400-33365800	Enhancers	Fetal Heart	heart
28	chr22:33363600-33364000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr22:33363600-33364000	Enhancers	Fetal Muscle Trunk	muscle
30	chr22:33363600-33364200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:33363600-33364200	Enhancers	Right Atrium	heart
32	chr22:33363800-33364000	Enhancers	Brain Hippocampus Middle	brain
33	chr22:33363800-33364000	Enhancers	Left Ventricle	heart
34	chr22:33363800-33364000	Enhancers	Lung	lung
35	chr22:33363800-33364000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
36	chr22:33363800-33364600	Enhancers	Pancreas	Pancrea
37	chr22:33363800-33365200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr22:33363800-33365400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr22:33363800-33365600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr22:33363800-33366800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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