Variant report

Variant	rs17287497
Chromosome Location	chr2:172351233-172351234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172349691..172351333-chr2:172358048..172359636,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10172434	0.95[EUR][1000 genomes]
rs12617802	0.92[CEU][hapmap]
rs12621138	0.87[CEU][hapmap]
rs16859368	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859371	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859373	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859377	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859404	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16859405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16859410	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17287442	0.94[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17287624	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1882378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3731984	0.81[ASN][1000 genomes]
rs3795996	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3806562	0.87[CEU][hapmap]
rs3806563	0.87[CEU][hapmap]
rs55711751	0.81[ASN][1000 genomes]
rs55715902	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56065525	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56239048	0.85[ASN][1000 genomes]
rs56273218	0.85[ASN][1000 genomes]
rs56302833	0.81[ASN][1000 genomes]
rs61021737	0.85[ASN][1000 genomes]
rs61502503	0.85[ASN][1000 genomes]
rs6759487	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs72882347	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72882358	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72882363	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73021048	0.85[ASN][1000 genomes]
rs884409	0.93[CEU][hapmap]
rs9646734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17287497	GAD1	cis	cerebellum	SCAN
rs17287497	CYBRD1	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172339800-172352200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:172340000-172368400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:172346000-172353000	Weak transcription	Primary T cells from cord blood	blood
4	chr2:172348600-172355000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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