Variant report

Variant	rs9589297
Chromosome Location	chr13:92226609-92226610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:91998717..92000233-chr13:92225643..92228118,2	K562	blood:
2	chr13:91998733..92001085-chr13:92225661..92228780,3	K562	blood:
3	chr13:92010873..92012565-chr13:92225020..92227817,2	K562	blood:
4	chr13:92220200..92222045-chr13:92225893..92228117,2	K562	blood:
5	chr13:92009349..92012461-chr13:92224404..92227397,3	K562	blood:

Variant related genes	Relation type
ENSG00000215417	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12583138	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1336208	0.90[CHB][hapmap]
rs1336219	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes]
rs1336220	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1414714	0.97[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1414715	1.00[CEU][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1414716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs1572433	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16946173	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs17483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953616	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes]
rs2065849	1.00[ASN][1000 genomes]
rs2065851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065852	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184728	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2351871	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs4143764	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs4359314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402419	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4771841	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4773638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493369	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap]
rs6492554	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7319303	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324772	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7332002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7490394	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7982049	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983224	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes]
rs7984663	1.00[ASN][1000 genomes]
rs7993829	0.95[CHB][hapmap]
rs870112	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870113	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301734	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9301738	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs945532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9515937	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9515939	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9515943	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515944	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9523346	0.88[CHB][hapmap]
rs9523348	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap]
rs9523351	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs9523352	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9523358	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs9523366	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9583946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9589295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9589296	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9589298	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9589299	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv562714	chr13:92056911-92304974	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1036860	chr13:92061347-92291771	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv562715	chr13:92061878-92299609	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1041168	chr13:92062057-92301861	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv949582	chr13:92062331-92301861	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1041762	chr13:92065459-92267509	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv541874	chr13:92065459-92267509	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv529091	chr13:92065460-92267510	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1045465	chr13:92065659-92267370	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv541875	chr13:92065659-92267370	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv531890	chr13:92065660-92267369	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1040707	chr13:92072034-92302281	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1045421	chr13:92075673-92283600	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv541876	chr13:92075673-92283600	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv530635	chr13:92084151-92280466	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1045669	chr13:92111663-92245308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv541878	chr13:92111663-92245308	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv562716	chr13:92128694-92250454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv562717	chr13:92135345-92250454	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1040709	chr13:92173603-92318362	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv2753383	chr13:92226599-92462699	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9589297	GPC5	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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