Variant report

Variant	rs10165864
Chromosome Location	chr2:55723038-55723039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55720808..55723210-chr2:55837791..55839820,2	MCF-7	breast:
2	chr2:55716556..55719523-chr2:55720351..55723403,5	K562	blood:
3	chr2:55716556..55719523-chr2:55721485..55723403,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10181648	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10454749	0.83[EUR][1000 genomes]
rs10460508	0.82[CEU][hapmap]
rs10496050	0.85[CEU][hapmap]
rs1058582	0.80[EUR][1000 genomes]
rs1084522	0.85[CEU][hapmap]
rs11125579	0.86[EUR][1000 genomes]
rs11679412	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17278044	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs17369191	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1823893	0.85[CEU][hapmap]
rs1975484	0.85[CEU][hapmap]
rs1975487	0.81[CEU][hapmap]
rs2586954	0.82[CEU][hapmap]
rs2627776	0.82[CEU][hapmap]
rs35504023	0.85[CEU][hapmap]
rs3762513	0.80[EUR][1000 genomes]
rs4290693	0.85[CEU][hapmap]
rs4672052	0.84[EUR][1000 genomes]
rs56333933	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165168	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165173	0.82[EUR][1000 genomes]
rs6545506	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs6739513	0.80[EUR][1000 genomes]
rs7582278	0.82[EUR][1000 genomes]
rs782568	0.82[CEU][hapmap]
rs782586	0.85[CEU][hapmap]
rs782588	0.85[CEU][hapmap]
rs782590	0.82[CEU][hapmap]
rs782595	0.85[CEU][hapmap]
rs782599	0.92[CEU][hapmap]
rs782602	0.96[CEU][hapmap]
rs782606	0.82[CEU][hapmap]
rs782652	0.82[CEU][hapmap]
rs9917139	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers 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	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv521318	chr2:55716650-55736704	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10165864	PNPT1	cis	cerebellum	SCAN
rs10165864	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs10165864	CCDC104	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55718600-55726800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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