Variant report

Variant	rs6888979
Chromosome Location	chr5:90335536-90335537
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	chr5:90335038..90337004-chr5:90346383..90348688,2	K562	blood:
2	chr5:90333269..90336003-chr5:90350864..90353414,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10074525	1.00[ASN][1000 genomes]
rs10514342	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs10514343	1.00[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738573	1.00[ASN][1000 genomes]
rs11743775	1.00[ASN][1000 genomes]
rs11744033	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs11744325	1.00[ASN][1000 genomes]
rs11949884	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11951675	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs11952993	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955946	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186968	1.00[ASN][1000 genomes]
rs12187656	1.00[ASN][1000 genomes]
rs12187790	1.00[ASN][1000 genomes]
rs12188068	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188094	1.00[ASN][1000 genomes]
rs12188249	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188655	1.00[ASN][1000 genomes]
rs12189005	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17571029	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs17572843	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633498	1.00[ASN][1000 genomes]
rs1976566	1.00[ASN][1000 genomes]
rs2438348	1.00[ASN][1000 genomes]
rs3114653	1.00[ASN][1000 genomes]
rs34243354	1.00[ASN][1000 genomes]
rs34381536	1.00[ASN][1000 genomes]
rs35060258	1.00[ASN][1000 genomes]
rs35299092	1.00[ASN][1000 genomes]
rs3850657	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55792004	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55941525	1.00[ASN][1000 genomes]
rs56051320	1.00[ASN][1000 genomes]
rs56099704	1.00[ASN][1000 genomes]
rs56106025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258383	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374052	1.00[ASN][1000 genomes]
rs62376462	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376463	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376490	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376491	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452927	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs66509877	1.00[ASN][1000 genomes]
rs6860216	1.00[ASN][1000 genomes]
rs6861614	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6880626	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886773	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs6888672	1.00[ASN][1000 genomes]
rs6889138	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784617	1.00[ASN][1000 genomes]
rs72784624	1.00[ASN][1000 genomes]
rs72784689	1.00[ASN][1000 genomes]
rs72784700	1.00[ASN][1000 genomes]
rs72784702	1.00[ASN][1000 genomes]
rs73771166	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7711168	1.00[ASN][1000 genomes]
rs7721862	1.00[ASN][1000 genomes]
rs7723305	1.00[ASN][1000 genomes]
rs949789	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6888979	GPR98	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:90330800-90338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90334400-90338800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:90334600-90338800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:90335000-90340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:90335000-90340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:90335000-90344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:90335200-90344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90335400-90338600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:90335400-90338600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:90335400-90340600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links