Variant report

Variant	rs7980136
Chromosome Location	chr12:59335248-59335249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10877188	1.00[EUR][1000 genomes]
rs10877198	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877200	0.83[EUR][1000 genomes]
rs11172823	0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11172824	0.80[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11172825	0.92[EUR][1000 genomes]
rs11172827	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172831	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172833	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172839	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172840	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172846	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172857	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172858	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172860	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172861	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172862	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172866	0.83[EUR][1000 genomes]
rs11172867	0.83[EUR][1000 genomes]
rs11172868	0.85[EUR][1000 genomes]
rs12368752	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12370522	0.82[EUR][1000 genomes]
rs12423502	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12424788	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12426212	0.92[EUR][1000 genomes]
rs12426969	0.92[EUR][1000 genomes]
rs17121828	0.83[EUR][1000 genomes]
rs55888651	0.83[EUR][1000 genomes]
rs58692617	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58997893	0.94[AFR][1000 genomes]
rs60522760	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60984323	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61754220	0.92[EUR][1000 genomes]
rs61919461	0.97[EUR][1000 genomes]
rs61919462	1.00[EUR][1000 genomes]
rs61919464	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61919465	1.00[EUR][1000 genomes]
rs61919466	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61919469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919471	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919513	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919518	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919519	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919520	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919521	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919523	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919524	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61919525	0.88[EUR][1000 genomes]
rs61919531	0.87[EUR][1000 genomes]
rs61919532	0.87[EUR][1000 genomes]
rs6581224	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136193	0.95[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7138401	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7294684	1.00[EUR][1000 genomes]
rs7297094	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7301299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302365	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303773	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7309872	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7963207	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7968111	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7969722	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970054	0.94[EUR][1000 genomes]
rs7980483	0.92[EUR][1000 genomes]
rs9645802	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7980136	PIP4K2C	cis	cerebellum	SCAN
rs7980136	DCTN2	cis	cerebellum	SCAN
rs7980136	MBD6	cis	cerebellum	SCAN
rs7980136	ESPL1	cis	cerebellum	SCAN
rs7980136	COQ10A	cis	cerebellum	SCAN
rs7980136	RAB5B	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59328600-59337000	Weak transcription	Gastric	stomach
2	chr12:59333800-59336400	Weak transcription	Stomach Mucosa	stomach
3	chr12:59334000-59335400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:59335200-59335400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:59335200-59336000	Flanking Active TSS	HUVEC	blood vessel
6	chr12:59335200-59337400	Enhancers	Fetal Intestine Small	intestine

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