Variant report

Variant	rs2904979
Chromosome Location	chr11:65000719-65000720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64999920..65001432-chr11:65190879..65192443,2	K562	blood:
2	chr11:64992394..64994754-chr11:64999110..65001538,2	MCF-7	breast:
3	chr11:64949057..64951072-chr11:64998711..65000957,2	MCF-7	breast:
4	chr11:64948798..64950759-chr11:64998900..65001890,2	MCF-7	breast:
5	chr11:64993421..64996189-chr11:64998607..65001730,3	K562	blood:

Variant related genes	Relation type
ENSG00000014216	Chromatin interaction
ENSG00000254614	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10750761	0.98[ASN][1000 genomes]
rs1195733	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1633466	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1783486	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]
rs1858783	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1877450	0.94[ASN][1000 genomes]
rs239257	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239261	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2904966	0.88[CEU][hapmap];0.97[GIH][hapmap]
rs2904967	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs2904980	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2904982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2904983	1.00[ASN][1000 genomes]
rs2904984	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2904986	0.83[ASN][1000 genomes]
rs2957111	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3015997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015999	0.87[ASN][1000 genomes]
rs3016001	0.96[ASN][1000 genomes]
rs3016002	0.94[ASN][1000 genomes]
rs482842	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs487989	0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap]
rs499027	0.83[ASN][1000 genomes]
rs503277	1.00[JPT][hapmap]
rs506280	1.00[JPT][hapmap]
rs507005	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs509303	0.89[CHD][hapmap];0.84[GIH][hapmap]
rs526502	0.84[CHD][hapmap];0.82[GIH][hapmap];0.83[ASN][1000 genomes]
rs541829	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554122	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs560097	0.80[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs571128	0.88[ASN][1000 genomes]
rs592050	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs611910	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs612392	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs620427	0.88[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap]
rs625427	1.00[ASN][1000 genomes]
rs626555	1.00[JPT][hapmap]
rs626802	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs630055	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs655433	1.00[JPT][hapmap]
rs667341	0.80[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs668735	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs673147	0.80[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs676114	0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap]
rs676573	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs689288	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs7111907	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7116674	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs8638	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	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2904979	POLA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64993600-65001400	Weak transcription	Right Ventricle	heart
2	chr11:64993600-65011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:64993800-65003800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:64993800-65004000	Weak transcription	Esophagus	oesophagus
5	chr11:64993800-65010800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:64993800-65010800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:64994000-65003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:64994200-65003800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:64994200-65007200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:64997200-65001800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:64997800-65003600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:64997800-65009400	Weak transcription	Fetal Intestine Small	intestine
13	chr11:64998000-65004000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:65000200-65000800	Enhancers	Lung	lung
15	chr11:65000400-65000800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:65000600-65000800	Enhancers	Gastric	stomach

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