Variant report

Variant	rs499027
Chromosome Location	chr11:65025878-65025879
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 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

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64878189..64880589-chr11:65025873..65028046,2	MCF-7	breast:
2	chr11:65017589..65019451-chr11:65025689..65027277,2	MCF-7	breast:
3	chr11:65022134..65027170-chr11:65027694..65031464,8	K562	blood:
4	chr11:64934217..64936652-chr11:65025702..65028546,2	K562	blood:
5	chr11:65024834..65026963-chr11:65027854..65029840,2	K562	blood:
6	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
ENSG00000254501	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000149809	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10750761	0.81[ASN][1000 genomes]
rs1152611	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1195733	0.89[EUR][1000 genomes]
rs12269727	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1633466	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783486	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858783	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2904979	0.83[ASN][1000 genomes]
rs2904980	0.83[ASN][1000 genomes]
rs2904981	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904983	0.83[ASN][1000 genomes]
rs2904986	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957111	0.83[ASN][1000 genomes]
rs3015997	0.83[ASN][1000 genomes]
rs3015999	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3016000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016001	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4149813	0.84[EUR][1000 genomes]
rs482842	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487397	0.83[ASN][1000 genomes]
rs487568	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs503277	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506280	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507005	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526502	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541829	0.80[ASN][1000 genomes]
rs560097	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571128	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs592050	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603286	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611910	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625427	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626555	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630055	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636928	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs650056	0.83[ASN][1000 genomes]
rs655433	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667341	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676573	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8638	0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs499027	POLA2	Cis_1M	lymphoblastoid	RTeQTL

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	chr11:65025600-65026200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:65025800-65028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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