Variant report

Variant	rs11955946
Chromosome Location	chr5:90344018-90344019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90343546..90347472-chr5:90675277..90677935,4	MCF-7	breast:
2	chr5:90337875..90340059-chr5:90342694..90345036,3	K562	blood:
3	chr5:90341629..90343575-chr5:90343795..90345327,2	K562	blood:
4	chr5:90343505..90346725-chr5:90355686..90358630,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

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];0.84[LWK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.89[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	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[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];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188094	1.00[ASN][1000 genomes]
rs12188249	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188655	1.00[ASN][1000 genomes]
rs12189005	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658697	1.00[YRI][hapmap]
rs13152882	1.00[YRI][hapmap]
rs17571029	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs17572843	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55792004	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258383	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374052	1.00[ASN][1000 genomes]
rs62376462	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376463	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376490	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6880626	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886773	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs6888672	1.00[ASN][1000 genomes]
rs6888979	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]
rs6889138	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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	0.95[AMR][1000 genomes];0.94[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]
rs951948	1.00[YRI][hapmap]

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
rs11955946	GPR98	cis	cerebellum	SCAN

Chromatin state (count:14 , 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	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:90341600-90344200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:90343200-90346200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:90343400-90344400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:90343400-90345200	Enhancers	A549	lung
7	chr5:90343600-90344600	Enhancers	Colon Smooth Muscle	Colon
8	chr5:90343800-90344800	Enhancers	Rectal Smooth Muscle	rectum
9	chr5:90343800-90345400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:90344000-90344400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:90344000-90344400	Enhancers	Adipose Nuclei	Adipose
12	chr5:90344000-90344600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:90344000-90344600	Enhancers	Liver	Liver
14	chr5:90344000-90344800	Enhancers	HUES48 Cell Line	embryonic stem cell

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