Variant report

Variant	rs2904981
Chromosome Location	chr11:65003026-65003027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64937641..64939607-chr11:65002371..65004553,2	K562	blood:
2	chr11:65001858..65003839-chr11:65008819..65010736,2	MCF-7	breast:
3	chr11:64996294..64998325-chr11:65001503..65003703,2	MCF-7	breast:
4	chr11:64998225..65000340-chr11:65001571..65004563,3	K562	blood:
5	chr11:64899743..64902690-chr11:65002264..65005486,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162298	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10750761	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1195733	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1633466	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783486	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858783	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1877450	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239257	0.96[ASN][1000 genomes]
rs239261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2904966	0.85[CEU][hapmap]
rs2904979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2904980	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[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2904983	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904984	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904985	0.86[EUR][1000 genomes]
rs2904986	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957110	0.87[AFR][1000 genomes]
rs2957111	1.00[ASN][1000 genomes]
rs3015997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3015999	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3016000	0.80[EUR][1000 genomes]
rs3016001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016002	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs482842	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs487568	0.81[EUR][1000 genomes]
rs488289	0.80[EUR][1000 genomes]
rs499027	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs507005	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs526502	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs541829	0.98[ASN][1000 genomes]
rs554122	0.86[CEU][hapmap]
rs560097	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs571128	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs592050	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs611910	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs612392	0.85[CEU][hapmap]
rs620427	0.85[CEU][hapmap]
rs625427	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626802	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6591180	1.00[CHB][hapmap]
rs667341	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs668735	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs673147	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs676573	0.86[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689288	0.85[CEU][hapmap]
rs7111907	0.94[ASN][1000 genomes]
rs7116674	1.00[CHB][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2904981	POLA2	cis	multi-tissue	Pritchard
rs2904981	POLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 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	chr11:64997800-65003600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:64997800-65009400	Weak transcription	Fetal Intestine Small	intestine
11	chr11:64998000-65004000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:65000800-65003800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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