Variant report

Variant	rs2904983
Chromosome Location	chr11:65005482-65005483
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	chr11:65004913..65006533-chr11:65033378..65036225,2	K562	blood:
2	chr11:64899743..64902690-chr11:65002264..65005486,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162298	Chromatin interaction
ENSG00000014138	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10750761	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1195733	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1633466	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783486	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877450	0.94[ASN][1000 genomes]
rs239257	0.96[ASN][1000 genomes]
rs239261	0.93[ASN][1000 genomes]
rs2904979	1.00[ASN][1000 genomes]
rs2904980	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2904981	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904982	0.85[ASN][1000 genomes]
rs2904984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904986	0.83[ASN][1000 genomes]
rs2957110	0.82[AFR][1000 genomes]
rs2957111	1.00[ASN][1000 genomes]
rs3015997	1.00[ASN][1000 genomes]
rs3015999	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3016001	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016002	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499027	0.83[ASN][1000 genomes]
rs526502	0.83[ASN][1000 genomes]
rs541829	0.98[ASN][1000 genomes]
rs571128	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs592050	0.83[ASN][1000 genomes]
rs625427	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626802	0.83[ASN][1000 genomes]
rs676573	0.83[ASN][1000 genomes]
rs7111907	0.94[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2904983	POLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 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	chr11:64994200-65007200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:64997800-65009400	Weak transcription	Fetal Intestine Small	intestine
6	chr11:65004000-65009200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:65004200-65005800	Enhancers	HepG2	liver
8	chr11:65004400-65009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:65004600-65006200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:65004600-65011200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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