Variant report

Variant	rs17863773
Chromosome Location	chr2:234573896-234573897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1042605	0.81[ASN][1000 genomes]
rs10929251	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10929252	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1113193	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs12053462	0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs12466747	0.82[AMR][1000 genomes]
rs12472689	0.84[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs12474215	0.82[AMR][1000 genomes]
rs12474980	0.84[LWK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs12476197	0.84[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs12479240	0.83[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17854828	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs17862847	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17862856	0.86[AMR][1000 genomes]
rs17862857	0.84[ASW][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs17863766	0.94[CEU][hapmap]
rs17864684	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17864686	0.82[AMR][1000 genomes]
rs17868303	0.81[ASN][1000 genomes]
rs17868325	0.84[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs17874938	0.81[ASN][1000 genomes]
rs1823803	0.82[JPT][hapmap]
rs1901813	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2248733	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs28946877	0.82[AMR][1000 genomes]
rs28969987	0.81[ASN][1000 genomes]
rs4114768	0.83[ASN][1000 genomes]
rs4485562	0.84[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs4663871	0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs4663877	0.82[AMR][1000 genomes]
rs6706988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713902	0.82[JPT][hapmap]
rs6728792	0.82[JPT][hapmap]
rs6731242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753317	0.82[AMR][1000 genomes]
rs7608713	0.81[CHD][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv876015	chr2:234518011-234579915	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv17839	chr2:234569283-234575116	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17863773	USP40	Cis_1M	lymphoblastoid	RTeQTL
rs17863773	FBXO36	cis	parietal	SCAN
rs17863773	SPP2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234554600-234587800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum

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