Variant report

Variant	rs2904980
Chromosome Location	chr11:65001679-65001680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64948798..64950759-chr11:64998900..65001890,2	MCF-7	breast:
2	chr11:64993421..64996189-chr11:64998607..65001730,3	K562	blood:
3	chr11:64996294..64998325-chr11:65001503..65003703,2	MCF-7	breast:
4	chr11:64998225..65000340-chr11:65001571..65004563,3	K562	blood:

Variant related genes	Relation type
ENSG00000254614	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10750761	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783486	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]
rs1858783	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap]
rs1877450	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239257	0.96[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2904966	0.85[GIH][hapmap]
rs2904967	0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs2904978	0.82[MEX][hapmap]
rs2904979	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2904981	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904982	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2904983	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2904984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904986	0.83[ASN][1000 genomes]
rs2957110	0.90[AFR][1000 genomes]
rs2957111	1.00[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[ASN][1000 genomes]
rs3015999	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3016001	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016002	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs482842	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs487989	0.90[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs499027	0.83[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs506280	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs507005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs509303	0.94[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap]
rs526502	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs541829	0.98[ASN][1000 genomes]
rs554122	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap]
rs560097	1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs571128	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs611910	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs620427	0.89[CHD][hapmap];0.85[GIH][hapmap]
rs625427	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs626802	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.83[ASN][1000 genomes]
rs630055	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs655433	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs667341	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs668735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap]
rs673147	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs676114	0.89[CHD][hapmap];0.85[GIH][hapmap]
rs676573	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7111907	0.94[ASN][1000 genomes]
rs7116674	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs8638	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2904980	POLA2	cis	multi-tissue	Pritchard
rs2904980	POLA2	cis	cerebellum	SCAN
rs2904980	GAL3ST3	cis	cerebellum	SCAN
rs2904980	PELI3	cis	parietal	SCAN
rs2904980	RPS6KB2	cis	cerebellum	SCAN
rs2904980	PLCB3	cis	cerebellum	SCAN
rs2904980	POLA2	cis	parietal	SCAN
rs2904980	POLA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 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	chr11:64993800-65003800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:64993800-65004000	Weak transcription	Esophagus	oesophagus
4	chr11:64993800-65010800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:64993800-65010800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:64994000-65003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:64994200-65003800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:64994200-65007200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:64997200-65001800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:64997800-65003600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:64997800-65009400	Weak transcription	Fetal Intestine Small	intestine
12	chr11:64998000-65004000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:65000800-65003800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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