Variant report

Variant	rs2904986
Chromosome Location	chr11:65031221-65031222
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 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	POLR2A	chr11:65030648-65031795	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:65031195-65031635	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65030468..65032005-chr11:65039331..65042158,2	K562	blood:
2	chr11:64947729..64951218-chr11:65027798..65031522,5	MCF-7	breast:
3	chr11:65029680..65031344-chr11:65031717..65033527,2	MCF-7	breast:
4	chr11:65028467..65031251-chr11:65099786..65102995,3	MCF-7	breast:
5	chr11:65009450..65011285-chr11:65030599..65032819,2	K562	blood:
6	chr11:64887057..64892358-chr11:65027493..65031887,5	K562	blood:
7	chr11:65029024..65031738-chr11:65081307..65084090,2	K562	blood:
8	chr11:65029710..65031446-chr11:65032712..65035703,3	K562	blood:
9	chr11:65029300..65032261-chr11:65099980..65102412,3	K562	blood:
10	chr11:65028603..65032064-chr11:65049175..65051003,3	MCF-7	breast:
11	chr11:65028586..65031401-chr11:65080311..65084684,5	MCF-7	breast:
12	chr11:65028264..65031673-chr11:65033494..65039309,8	MCF-7	breast:
13	chr11:64883613..64891269-chr11:65027573..65033885,11	K562	blood:
14	chr11:65027521..65031518-chr11:65033688..65038913,7	MCF-7	breast:

No data

Variant related genes	Relation type
POLA2	TF binding region
ENSG00000149806	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10750761	0.81[ASN][1000 genomes]
rs1152611	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1195733	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12269727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1633466	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783486	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858783	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28781278	0.85[AMR][1000 genomes]
rs2904979	0.83[ASN][1000 genomes]
rs2904980	0.83[ASN][1000 genomes]
rs2904981	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904983	0.83[ASN][1000 genomes]
rs2957111	0.83[ASN][1000 genomes]
rs3015997	0.83[ASN][1000 genomes]
rs3015999	0.87[ASN][1000 genomes]
rs3016000	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016001	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4149813	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs482842	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487397	0.83[ASN][1000 genomes]
rs487568	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503277	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506280	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507005	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526502	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541829	0.80[ASN][1000 genomes]
rs560097	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571128	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs592050	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603286	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611910	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625427	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626555	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630055	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636928	0.86[EUR][1000 genomes]
rs650056	0.83[ASN][1000 genomes]
rs655433	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667341	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676573	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8638	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2904986	POLA2	cis	multi-tissue	Pritchard
rs2904986	POLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65028800-65031400	Active TSS	GM12878-XiMat	blood
2	chr11:65030000-65044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:65030200-65058800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:65030400-65042800	Weak transcription	Stomach Mucosa	stomach
5	chr11:65030600-65031400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:65030600-65031400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:65030600-65031400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:65030600-65031400	Enhancers	Fetal Muscle Leg	muscle
9	chr11:65030600-65031600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr11:65030600-65031600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:65030600-65031600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:65030600-65032000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr11:65030600-65032200	Enhancers	HepG2	liver
14	chr11:65030600-65032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:65030600-65033000	Weak transcription	Thymus	Thymus
16	chr11:65030600-65033200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:65030600-65033200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:65030600-65033200	Weak transcription	NHDF-Ad	bronchial
19	chr11:65030600-65033400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr11:65030600-65033400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:65030600-65033400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:65030600-65033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:65030600-65033600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:65030600-65033600	Weak transcription	Osteobl	bone
25	chr11:65030600-65033800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:65030600-65034000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:65030600-65034000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:65030600-65034000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:65030600-65034000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:65030600-65034600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:65030600-65034600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:65030600-65034800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:65030600-65034800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:65030600-65034800	Weak transcription	Placenta	Placenta
35	chr11:65030600-65034800	Weak transcription	NHLF	lung
36	chr11:65030600-65035000	Weak transcription	Fetal Intestine Large	intestine
37	chr11:65030600-65036200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:65030600-65036200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:65030600-65036200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:65030600-65036200	Weak transcription	Fetal Kidney	kidney
41	chr11:65030600-65036200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:65030600-65036400	Weak transcription	Brain Anterior Caudate	brain
43	chr11:65030600-65036400	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:65030600-65036400	Weak transcription	Left Ventricle	heart
45	chr11:65030600-65037000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:65030600-65037600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:65030600-65037600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:65030600-65037600	Weak transcription	Fetal Brain Female	brain
49	chr11:65030600-65037600	Weak transcription	Ovary	ovary
50	chr11:65030600-65037600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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