Variant report

Variant	rs234302
Chromosome Location	chr19:40524872-40524873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:40524310-40528109	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:40524238-40526515	MCF10A-Er-Src	breast:	n/a	n/a
3	REST	chr19:40524150-40527833	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:40524393-40524994	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:40524708-40525330	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:40517320-40525363	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
ENSG00000268166	TF binding region

Extended variants
information (count: 167 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs1007628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10406738	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10417013	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10417043	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418196	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11542840	0.96[ASN][1000 genomes]
rs1327185	0.85[JPT][hapmap]
rs1327193	0.85[JPT][hapmap]
rs13344062	0.84[ASN][1000 genomes]
rs163213	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16973950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs170901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs173061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17796769	0.96[ASN][1000 genomes]
rs17796901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17797100	0.86[JPT][hapmap]
rs183504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs186801	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs186815	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1926931	0.90[ASN][1000 genomes]
rs1926932	0.90[ASN][1000 genomes]
rs1926933	0.90[ASN][1000 genomes]
rs1926934	0.90[ASN][1000 genomes]
rs2111543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2111544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2231737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs234301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234303	0.94[ASN][1000 genomes]
rs234304	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234306	0.92[ASN][1000 genomes]
rs234308	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs234309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234310	0.92[ASN][1000 genomes]
rs234313	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234314	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs234315	0.97[ASN][1000 genomes]
rs234317	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234318	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234326	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234328	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234343	0.91[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234355	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs234356	0.94[ASN][1000 genomes]
rs234357	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234360	0.92[ASN][1000 genomes]
rs234361	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234370	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234371	0.92[ASN][1000 genomes]
rs234374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs24135	0.86[JPT][hapmap]
rs24136	0.85[JPT][hapmap]
rs24137	0.86[JPT][hapmap]
rs2542303	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2569640	0.86[JPT][hapmap]
rs2569641	0.86[JPT][hapmap]
rs2569650	0.85[JPT][hapmap]
rs2767604	0.85[JPT][hapmap]
rs2767607	0.85[JPT][hapmap]
rs2819956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28366011	0.97[ASN][1000 genomes]
rs2915972	0.85[JPT][hapmap]
rs2986595	0.90[ASN][1000 genomes]
rs3000956	0.89[ASN][1000 genomes]
rs337779	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs337784	0.86[JPT][hapmap]
rs337785	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs337786	0.86[JPT][hapmap]
rs337787	0.86[JPT][hapmap]
rs337789	0.85[JPT][hapmap]
rs337792	0.85[JPT][hapmap]
rs337793	0.86[JPT][hapmap]
rs337794	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs337798	0.86[ASN][1000 genomes]
rs337799	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs337800	0.85[ASN][1000 genomes]
rs337801	0.82[ASN][1000 genomes]
rs34466648	0.91[CHB][hapmap]
rs365055	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs371500	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs372599	0.96[ASN][1000 genomes]
rs3760920	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs387202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3887029	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs392958	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3930885	0.97[ASN][1000 genomes]
rs404754	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs416283	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs420579	0.89[ASN][1000 genomes]
rs421533	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs423545	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs424353	0.92[ASN][1000 genomes]
rs426950	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4577216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs459091	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs57219798	0.96[ASN][1000 genomes]
rs57880771	0.90[ASN][1000 genomes]
rs57900299	0.91[ASN][1000 genomes]
rs58210425	0.95[ASN][1000 genomes]
rs58284735	0.95[ASN][1000 genomes]
rs58395013	0.92[ASN][1000 genomes]
rs58440570	0.90[ASN][1000 genomes]
rs58844095	0.82[ASN][1000 genomes]
rs58941665	0.95[ASN][1000 genomes]
rs59502139	0.92[ASN][1000 genomes]
rs59925663	0.96[ASN][1000 genomes]
rs60080503	0.91[ASN][1000 genomes]
rs60449727	0.91[ASN][1000 genomes]
rs60887294	0.97[ASN][1000 genomes]
rs61236589	0.97[ASN][1000 genomes]
rs61385499	1.00[ASN][1000 genomes]
rs615215	0.92[ASN][1000 genomes]
rs7247527	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7257747	0.91[ASN][1000 genomes]
rs7258202	0.91[ASN][1000 genomes]
rs7258506	0.92[ASN][1000 genomes]
rs7258627	0.92[ASN][1000 genomes]
rs7258778	0.91[ASN][1000 genomes]
rs7258974	0.90[ASN][1000 genomes]
rs7259855	0.90[ASN][1000 genomes]
rs7260378	0.90[ASN][1000 genomes]
rs73543974	0.96[ASN][1000 genomes]
rs73543979	0.96[ASN][1000 genomes]
rs73544000	0.82[ASN][1000 genomes]
rs73545909	0.97[ASN][1000 genomes]
rs73545911	0.97[ASN][1000 genomes]
rs73545934	0.97[ASN][1000 genomes]
rs73545936	0.97[ASN][1000 genomes]
rs73545938	0.97[ASN][1000 genomes]
rs73545945	0.97[ASN][1000 genomes]
rs73545950	0.97[ASN][1000 genomes]
rs73545955	0.97[ASN][1000 genomes]
rs73545975	0.97[ASN][1000 genomes]
rs73546001	0.97[ASN][1000 genomes]
rs73546002	0.97[ASN][1000 genomes]
rs73547618	0.97[ASN][1000 genomes]
rs73547620	0.97[ASN][1000 genomes]
rs73547638	0.97[ASN][1000 genomes]
rs73547652	1.00[ASN][1000 genomes]
rs73547656	1.00[ASN][1000 genomes]
rs73547663	1.00[ASN][1000 genomes]
rs73547676	1.00[ASN][1000 genomes]
rs73547677	1.00[ASN][1000 genomes]
rs73547696	0.95[ASN][1000 genomes]
rs73547702	0.95[ASN][1000 genomes]
rs73549804	0.92[ASN][1000 genomes]
rs73549810	0.92[ASN][1000 genomes]
rs73549811	0.92[ASN][1000 genomes]
rs73549820	0.92[ASN][1000 genomes]
rs73549821	0.86[ASN][1000 genomes]
rs73549825	0.90[ASN][1000 genomes]
rs73549826	0.90[ASN][1000 genomes]
rs73549829	0.90[ASN][1000 genomes]
rs73549833	0.90[ASN][1000 genomes]
rs73549835	0.90[ASN][1000 genomes]
rs73549836	0.90[ASN][1000 genomes]
rs8105066	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8106032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8108793	0.89[ASN][1000 genomes]
rs9783938	0.87[ASN][1000 genomes]
rs9917073	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs234302	FCGBP	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40504000-40533800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:40512000-40527200	ZNF genes & repeats	Liver	Liver
3	chr19:40521200-40540800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:40524400-40525000	ZNF genes & repeats	Brain Anterior Caudate	brain
5	chr19:40524400-40525000	ZNF genes & repeats	A549	lung
6	chr19:40524600-40529400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links