Variant report

Variant	rs526502
Chromosome Location	chr11:65026590-65026591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65022945-65033166	K562	blood:	n/a	n/a
2	TEAD4	chr11:65026519-65026735	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr11:65026525-65026824	H1-hESC	embryonic stem cell:	n/a	chr11:65026631-65026643
4	YY1	chr11:65026519-65026829	H1-hESC	embryonic stem cell:	n/a	chr11:65026631-65026643

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64878189..64880589-chr11:65025873..65028046,2	MCF-7	breast:
2	chr11:64901495..64903969-chr11:65026515..65030932,5	MCF-7	breast:
3	chr11:64879243..64883054-chr11:65026482..65029082,4	MCF-7	breast:
4	chr11:65017589..65019451-chr11:65025689..65027277,2	MCF-7	breast:
5	chr11:65022134..65027170-chr11:65027694..65031464,8	K562	blood:
6	chr11:64850072..64852972-chr11:65026497..65029318,2	K562	blood:
7	chr11:64934217..64936652-chr11:65025702..65028546,2	K562	blood:
8	chr11:65024834..65026963-chr11:65027854..65029840,2	K562	blood:
9	chr11:65025183..65028545-chr11:65033759..65036797,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP003068.23.1-1	chr11:65023535-65027669	ucscGeneNc_uc001ody_2

No data

Variant related genes	Relation type
POLA2	TF binding region
ENSG00000149809	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000162300	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10750761	0.81[ASN][1000 genomes]
rs1152611	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1195733	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12269727	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1633466	0.91[CEU][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783486	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]
rs1858783	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs28781278	0.89[AMR][1000 genomes]
rs2904966	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs2904967	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap]
rs2904979	0.84[CHD][hapmap];0.82[GIH][hapmap];0.83[ASN][1000 genomes]
rs2904980	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]
rs2904981	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904983	0.83[ASN][1000 genomes]
rs2904984	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2904986	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957111	0.83[ASN][1000 genomes]
rs3015997	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs3015999	0.87[ASN][1000 genomes]
rs3016000	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016001	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482842	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487397	0.83[ASN][1000 genomes]
rs487568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503277	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506280	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507005	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541829	0.80[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs560097	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571128	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs592050	0.91[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603286	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611910	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs620427	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap]
rs625427	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626555	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630055	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636928	0.84[EUR][1000 genomes]
rs650056	0.83[ASN][1000 genomes]
rs655433	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667341	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap]
rs676573	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116674	0.89[CHD][hapmap]
rs8638	1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs526502	POLA2	cis	cerebellum	SCAN
rs526502	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs526502	POLA2	cis	lymphoblastoid	seeQTL
rs526502	POLA2	cis	parietal	SCAN
rs526502	RPS6KB2	cis	cerebellum	SCAN
rs526502	PLCB3	cis	cerebellum	SCAN
rs526502	BATF2	cis	cerebellum	SCAN
rs526502	GAL3ST3	cis	cerebellum	SCAN
rs526502	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65015200-65028600	Weak transcription	Fetal Intestine Small	intestine
2	chr11:65016400-65028600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:65018400-65028600	Weak transcription	Liver	Liver
4	chr11:65019600-65028400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:65022800-65028600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:65023000-65026800	Weak transcription	HepG2	liver
7	chr11:65023800-65028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:65024400-65028800	Weak transcription	Pancreas	Pancrea
9	chr11:65025800-65028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:65026200-65028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links