Variant report

Variant	rs4409759
Chromosome Location	chr10:97575579-97575580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10159941	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10748639	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10748640	0.81[ASN][1000 genomes]
rs10748641	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10786230	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10786235	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786238	0.88[ASN][1000 genomes]
rs10882653	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10882670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882681	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882682	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10882683	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1113881	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11188459	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188468	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11188470	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188485	0.88[ASN][1000 genomes]
rs11188488	0.88[ASN][1000 genomes]
rs11498722	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11528098	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12240959	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933166	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1933171	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1953710	0.82[ASN][1000 genomes]
rs2225894	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2901874	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176883	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3938778	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4075311	0.89[AFR][1000 genomes]
rs4457685	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4641390	0.91[EUR][1000 genomes]
rs4917700	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4917701	0.80[AFR][1000 genomes]
rs4918958	0.81[ASN][1000 genomes]
rs4918964	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60227189	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584014	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6584015	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6584026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6584028	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6584031	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6584033	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7069234	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073723	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7073973	0.81[ASN][1000 genomes]
rs7081414	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7090320	0.88[ASN][1000 genomes]
rs7098750	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7100137	0.90[ASN][1000 genomes]
rs7897988	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7901116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7905653	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7910565	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7911400	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7912508	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7919773	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs951418	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97553000-97576200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:97570400-97577600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:97573000-97575800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:97573000-97575800	Enhancers	Brain Hippocampus Middle	brain
5	chr10:97573200-97575800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:97573200-97575800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr10:97573200-97580000	Enhancers	HUVEC	blood vessel
8	chr10:97573400-97575800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr10:97573800-97584400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:97574000-97575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:97574200-97575600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:97574200-97583000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:97574400-97575600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:97574400-97575600	Weak transcription	Placenta	Placenta
15	chr10:97574400-97575600	Weak transcription	Left Ventricle	heart
16	chr10:97574400-97576800	Weak transcription	Fetal Stomach	stomach
17	chr10:97574400-97578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:97574400-97578200	Weak transcription	Right Ventricle	heart
19	chr10:97574400-97580800	Weak transcription	Small Intestine	intestine
20	chr10:97574400-97581000	Weak transcription	Spleen	Spleen
21	chr10:97574400-97581400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:97574600-97575800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:97574600-97576400	Weak transcription	Primary B cells from cord blood	blood
24	chr10:97574600-97578200	Weak transcription	NHLF	lung
25	chr10:97574600-97578400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:97574800-97575800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:97574800-97578200	Weak transcription	HMEC	breast
28	chr10:97574800-97590800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:97575000-97575600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:97575000-97575800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr10:97575000-97577400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:97575000-97580400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:97575200-97575600	Weak transcription	Esophagus	oesophagus
34	chr10:97575200-97575600	Bivalent Enhancer	HepG2	liver
35	chr10:97575200-97575800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:97575200-97575800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr10:97575200-97576000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr10:97575200-97576000	Enhancers	Adipose Nuclei	Adipose
39	chr10:97575200-97576400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr10:97575200-97577000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr10:97575400-97575600	Enhancers	Aorta	Aorta
42	chr10:97575400-97575600	Strong transcription	GM12878-XiMat	blood
43	chr10:97575400-97575800	Enhancers	Lung	lung
44	chr10:97575400-97579400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr10:97575400-97579600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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