Variant report

Variant	rs9568603
Chromosome Location	chr13:52034271-52034272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs17075688	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17194948	0.90[CEU][hapmap]
rs17195020	0.90[CEU][hapmap]
rs2026526	0.96[EUR][1000 genomes]
rs2026527	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274061	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2274929	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs3825524	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs6561634	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73197809	0.84[EUR][1000 genomes]
rs73197821	0.98[EUR][1000 genomes]
rs73197824	0.89[EUR][1000 genomes]
rs73197826	0.94[EUR][1000 genomes]
rs7333661	0.82[ASN][1000 genomes]
rs7335122	0.89[CEU][hapmap]
rs7335141	0.81[ASN][1000 genomes]
rs7335144	0.80[EUR][1000 genomes]
rs7337450	0.90[CEU][hapmap]
rs7989674	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7989850	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7996243	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs7998084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8001311	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001787	0.83[ASN][1000 genomes]
rs9316537	0.95[YRI][hapmap]
rs9316539	0.82[ASN][1000 genomes]
rs9316541	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9316545	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9316546	0.96[EUR][1000 genomes]
rs9526752	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs9526754	0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs9526757	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9526759	0.80[EUR][1000 genomes]
rs9526761	0.84[EUR][1000 genomes]
rs9526764	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526768	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535645	0.82[CEU][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs9535646	0.90[CEU][hapmap]
rs9535652	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs9535653	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs9535655	0.89[CEU][hapmap]
rs9535660	0.89[CEU][hapmap]
rs9535661	0.90[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs9535662	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9535663	0.90[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs9535665	0.90[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535669	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535670	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535671	0.98[EUR][1000 genomes]
rs9535672	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535673	1.00[ASN][1000 genomes]
rs9535674	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535677	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535678	0.93[EUR][1000 genomes]
rs9535679	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535680	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs9535682	0.95[EUR][1000 genomes]
rs9535683	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535687	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535688	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535689	0.94[EUR][1000 genomes]
rs9535690	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535693	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535694	0.89[EUR][1000 genomes]
rs9535696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535697	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9535699	0.90[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs9563046	0.90[CEU][hapmap]
rs9568600	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568608	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568612	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9634842	0.87[CEU][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv977240	chr13:52033195-52035408	Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9568603	DDX26	cis	multi-tissue	Pritchard
rs9568603	ITM2B	cis	cerebellum	SCAN
rs9568603	CKAP2	cis	parietal	SCAN
rs9568603	WDFY2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52028600-52036000	Weak transcription	HSMMtube	muscle
2	chr13:52030400-52035200	Weak transcription	HSMM	muscle
3	chr13:52030600-52035800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr13:52030600-52036000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr13:52030600-52038800	Weak transcription	HepG2	liver
6	chr13:52030800-52034400	Weak transcription	Adipose Nuclei	Adipose
7	chr13:52030800-52035400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr13:52030800-52035400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr13:52030800-52036000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:52030800-52036000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:52030800-52036200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr13:52030800-52036200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr13:52031000-52036000	Weak transcription	Esophagus	oesophagus
14	chr13:52031000-52039800	Weak transcription	A549	lung
15	chr13:52031000-52044800	Weak transcription	Liver	Liver
16	chr13:52031200-52035800	Weak transcription	Primary T cells from cord blood	blood
17	chr13:52031200-52036200	Weak transcription	Gastric	stomach
18	chr13:52031200-52041400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:52031400-52034800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:52031400-52035800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:52031400-52036200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:52031400-52036200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr13:52031400-52036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:52031400-52036800	Weak transcription	Fetal Stomach	stomach
25	chr13:52031400-52037000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:52031600-52034400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr13:52031600-52035800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr13:52031600-52036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:52031600-52041600	Weak transcription	Pancreas	Pancrea
30	chr13:52031800-52035800	Weak transcription	Fetal Muscle Leg	muscle
31	chr13:52031800-52045400	Weak transcription	Primary B cells from cord blood	blood
32	chr13:52032000-52035400	Weak transcription	Spleen	Spleen
33	chr13:52034000-52034800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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