Variant report

Variant	rs9526825
Chromosome Location	chr13:52609193-52609194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52600061..52602835-chr13:52607989..52610209,4	K562	blood:
2	chr13:52603093..52604723-chr13:52608557..52611141,2	K562	blood:
3	chr13:52598398..52600067-chr13:52607293..52609530,2	K562	blood:

Variant related genes	Relation type
ENSG00000253797	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1004576	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1055062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1060631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134727	0.91[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap]
rs12146904	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12560598	0.91[ASN][1000 genomes]
rs1571189	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs1886539	0.90[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1886544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1886545	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886546	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147359	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147360	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147361	0.83[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2277448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408546	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408547	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408548	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2408554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2408609	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897964	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897965	0.88[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3742289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742291	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783242	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3818422	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264295	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4497567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4600369	0.86[ASN][1000 genomes]
rs4941720	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4941723	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4941727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4943060	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61958804	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61958805	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561658	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs6650384	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6650385	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66849828	0.86[ASN][1000 genomes]
rs7318287	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7319784	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7320252	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7320429	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs732071	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7320831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7321310	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7321435	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7321775	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7324458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap]
rs7332272	0.81[ASN][1000 genomes]
rs7332356	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7338131	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7981904	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7991237	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7998770	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap]
rs9526817	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526819	0.87[CHB][hapmap]
rs9526823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526826	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526834	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526835	0.88[ASN][1000 genomes]
rs9526836	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9526843	0.90[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535813	0.86[ASN][1000 genomes]
rs9535816	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535821	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535822	0.86[CHB][hapmap]
rs9535824	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535825	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9535826	0.87[CHB][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535845	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535853	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535861	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535871	0.87[ASN][1000 genomes]
rs9535873	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535883	0.82[ASN][1000 genomes]
rs9535885	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535889	0.85[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9568682	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568684	0.95[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568692	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9526825	NCRNA00282	cis	cerebellum	SCAN
rs9526825	CKAP2	cis	parietal	SCAN
rs9526825	TIA1	trans	parietal	SCAN
rs9526825	LOC440138	cis	multi-tissue	Pritchard
rs9526825	NEK3	cis	cerebellum	SCAN
rs9526825	NEK5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52588000-52609200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52588000-52617400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:52595000-52611200	Weak transcription	Psoas Muscle	Psoas
4	chr13:52596600-52614000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:52599000-52611000	Weak transcription	Fetal Brain Male	brain
6	chr13:52600000-52609800	Weak transcription	Stomach Mucosa	stomach
7	chr13:52600200-52613800	Weak transcription	Colon Smooth Muscle	Colon
8	chr13:52600200-52613800	Weak transcription	Small Intestine	intestine
9	chr13:52600400-52627600	Weak transcription	HSMMtube	muscle
10	chr13:52600800-52609600	Weak transcription	Esophagus	oesophagus
11	chr13:52600800-52611400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:52601000-52619400	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:52601200-52609400	Weak transcription	HMEC	breast
14	chr13:52601200-52610000	Weak transcription	Primary B cells from cord blood	blood
15	chr13:52601600-52609600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:52603200-52613400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:52603600-52610000	Weak transcription	Fetal Kidney	kidney
18	chr13:52603600-52610200	Weak transcription	Left Ventricle	heart
19	chr13:52603800-52609600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr13:52603800-52610200	Weak transcription	Gastric	stomach
21	chr13:52604000-52612400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:52604000-52615200	Weak transcription	Fetal Intestine Large	intestine
23	chr13:52604200-52610200	Weak transcription	K562	blood
24	chr13:52604200-52610800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:52604200-52611600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:52604200-52613400	Weak transcription	Right Ventricle	heart
27	chr13:52604400-52609600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:52604400-52610400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:52604400-52611000	Weak transcription	Primary T cells from cord blood	blood
30	chr13:52604400-52612000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:52605200-52609600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:52605400-52611800	Weak transcription	Fetal Thymus	thymus
33	chr13:52605800-52614400	Weak transcription	Thymus	Thymus
34	chr13:52606000-52609400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:52606000-52615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:52606000-52618000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:52608800-52610200	Weak transcription	Pancreas	Pancrea
38	chr13:52609000-52609400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr13:52609000-52610600	Enhancers	HepG2	liver

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