Variant report

Variant	rs1783486
Chromosome Location	chr11:65008917-65008918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65008228..65010654-chr11:65264874..65266459,2	MCF-7	breast:
2	chr11:65001858..65003839-chr11:65008819..65010736,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10750761	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858783	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1877450	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs239257	0.91[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs2904966	0.85[GIH][hapmap]
rs2904967	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs2904979	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.96[ASN][1000 genomes]
rs2904980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904981	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904982	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2904983	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904985	0.84[EUR][1000 genomes]
rs2904986	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957111	0.96[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.96[ASN][1000 genomes]
rs3015999	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3016000	0.82[EUR][1000 genomes]
rs3016001	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016002	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs482842	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs487568	0.81[EUR][1000 genomes]
rs487989	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap]
rs488289	0.80[EUR][1000 genomes]
rs499027	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs506280	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs507005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs509303	0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap]
rs526502	0.91[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs541829	0.93[ASN][1000 genomes]
rs554122	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs560097	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs571128	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs611910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs620427	0.89[CHD][hapmap];0.85[GIH][hapmap]
rs625427	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs626802	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs630055	0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs655433	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs667341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs668735	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs673147	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs676114	0.89[CHD][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap]
rs676573	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7111907	0.90[ASN][1000 genomes]
rs7116674	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[YRI][hapmap]
rs8638	0.88[CEU][hapmap];1.00[JPT][hapmap]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv976461	chr11:65000821-65054446	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1783486	PLCB3	cis	cerebellum	SCAN
rs1783486	POLA2	cis	parietal	SCAN
rs1783486	POLA2	cis	lymphoblastoid	seeQTL
rs1783486	POLA2	cis	cerebellum	SCAN
rs1783486	GAL3ST3	cis	cerebellum	SCAN
rs1783486	POLA2	cis	multi-tissue	Pritchard
rs1783486	RPS6KB2	cis	cerebellum	SCAN
rs1783486	BATF2	cis	cerebellum	SCAN
rs1783486	POLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64993600-65011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:64993800-65010800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr11:64993800-65010800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:64997800-65009400	Weak transcription	Fetal Intestine Small	intestine
5	chr11:65004000-65009200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:65004400-65009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:65004600-65011200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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