Variant report

Variant	rs9540960
Chromosome Location	chr13:67536618-67536619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1022866	1.00[JPT][hapmap]
rs10492596	1.00[JPT][hapmap]
rs10492597	1.00[JPT][hapmap]
rs11148738	1.00[JPT][hapmap]
rs1323911	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1323917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323923	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1408170	1.00[JPT][hapmap]
rs17195266	1.00[JPT][hapmap]
rs17587572	1.00[JPT][hapmap]
rs17791001	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs17791056	1.00[JPT][hapmap]
rs1924309	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1924310	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs260139	1.00[JPT][hapmap]
rs260140	1.00[JPT][hapmap]
rs260160	1.00[JPT][hapmap]
rs260168	1.00[JPT][hapmap]
rs61959219	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7981987	1.00[JPT][hapmap]
rs7987190	1.00[JPT][hapmap]
rs7987478	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9317632	0.86[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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9317633	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9317637	1.00[JPT][hapmap]
rs9529158	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9529163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9529170	1.00[JPT][hapmap]
rs9529174	1.00[JPT][hapmap]
rs9529180	1.00[JPT][hapmap]
rs9529181	1.00[JPT][hapmap]
rs9540946	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9540947	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9540949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9540950	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9540952	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9540953	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9540954	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9540956	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540958	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540959	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540967	1.00[JPT][hapmap]
rs9540971	1.00[JPT][hapmap]
rs9540983	1.00[JPT][hapmap]
rs9540988	1.00[JPT][hapmap]
rs9540993	1.00[JPT][hapmap]
rs9540995	1.00[JPT][hapmap]
rs9540996	1.00[JPT][hapmap]
rs9571705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv900407	chr13:67434161-67603745	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv832640	chr13:67460304-67635966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv428604	chr13:67480426-67645030	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv900411	chr13:67511430-67546608	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv900412	chr13:67512877-67572221	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv900413	chr13:67515590-67550301	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv900414	chr13:67515590-67701341	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1045093	chr13:67517932-67693875	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv541821	chr13:67517932-67693875	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv900415	chr13:67521014-67542554	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67531400-67538200	Weak transcription	A549	lung
2	chr13:67532600-67542000	Weak transcription	Brain Anterior Caudate	brain
3	chr13:67532600-67542000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr13:67533000-67538200	Weak transcription	Brain Angular Gyrus	brain
5	chr13:67533000-67539600	Weak transcription	Brain Substantia Nigra	brain
6	chr13:67533200-67538600	Weak transcription	Brain Cingulate Gyrus	brain

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