Variant report

Variant	rs17796901
Chromosome Location	chr19:40534637-40534638
allele	A/C
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	POLR2A	chr19:40531707-40536932	PANC-1	pancreas:	n/a	n/a
2	REST	chr19:40531505-40536927	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:40528255-40543887	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
ENSG00000269069	TF binding region

Extended variants
information (count: 170 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:168)

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	0.97[ASN][1000 genomes]
rs10417043	0.97[ASN][1000 genomes]
rs10418196	0.96[ASN][1000 genomes]
rs11542840	0.96[ASN][1000 genomes]
rs1327185	0.86[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap]
rs1327193	0.82[JPT][hapmap];0.86[YRI][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]
rs170900	0.81[CHD][hapmap]
rs170901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs173061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17796769	0.96[ASN][1000 genomes]
rs17797100	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs183504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs186801	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];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2111544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];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];0.97[ASN][1000 genomes]
rs234302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	0.94[ASN][1000 genomes]
rs234309	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs234310	0.92[ASN][1000 genomes]
rs234313	0.97[ASN][1000 genomes]
rs234314	0.82[ASN][1000 genomes]
rs234315	0.97[ASN][1000 genomes]
rs234317	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];0.97[ASN][1000 genomes]
rs234324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs234325	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs234326	0.97[ASN][1000 genomes]
rs234328	0.97[ASN][1000 genomes]
rs234341	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs234355	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs234356	0.94[ASN][1000 genomes]
rs234357	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];0.93[CHD][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];0.97[ASN][1000 genomes]
rs24135	0.85[JPT][hapmap]
rs24136	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs24137	0.85[JPT][hapmap]
rs2542303	0.97[ASN][1000 genomes]
rs2569640	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs2569641	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs2569650	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2767604	0.87[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs2767607	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs2819956	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28366011	0.97[ASN][1000 genomes]
rs2915972	0.87[CHD][hapmap];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	0.85[JPT][hapmap]
rs337785	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs337786	0.85[JPT][hapmap]
rs337787	0.84[JPT][hapmap]
rs337789	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs337792	0.87[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs337793	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs337794	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs337798	0.86[ASN][1000 genomes]
rs337799	0.92[CHB][hapmap];0.93[CHD][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];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs365055	0.97[ASN][1000 genomes]
rs371500	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs372599	0.96[ASN][1000 genomes]
rs3760920	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs387202	1.00[CHB][hapmap];1.00[JPT][hapmap];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	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs404754	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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs423545	0.95[ASN][1000 genomes]
rs424353	0.92[ASN][1000 genomes]
rs426950	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4577216	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs459091	0.92[CHB][hapmap];0.93[CHD][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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61236589	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61385499	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs615215	0.92[ASN][1000 genomes]
rs61737024	1.00[EUR][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	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73545934	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73545936	0.97[ASN][1000 genomes]
rs73545938	0.97[ASN][1000 genomes]
rs73545945	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73545950	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73545955	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73545975	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73546001	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73546002	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73547618	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73547620	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73547638	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73547652	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547656	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547663	0.89[AMR][1000 genomes];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	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8106032	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:2 , 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
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17796901	FCGBP	cis	lymphoblastoid	seeQTL
rs17796901	ZNF780A	cis	lymphoblastoid	seeQTL
rs17796901	FCGBP	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40521200-40540800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:40528600-40543800	ZNF genes & repeats	Liver	Liver
3	chr19:40529000-40543800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:40529200-40543800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:40529200-40543800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:40530600-40543800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:40532600-40535000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr19:40533600-40535200	ZNF genes & repeats	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links