Variant report

Variant	rs592050
Chromosome Location	chr11:65030189-65030190
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 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	MTA3	chr11:65028405-65030309	GM12878	blood:	n/a	n/a
3	STAT5A	chr11:65029750-65030366	GM12878	blood:	n/a	chr11:65029909-65029920
4	POLR2A	chr11:65028462-65030289	MCF-7	breast:	n/a	n/a
5	ZNF263	chr11:65029232-65030539	HEK293-T-REx	kidney:	n/a	chr11:65030227-65030236
6	NRF1	chr11:65030118-65030264	K562	blood:	n/a	n/a
7	HCFC1	chr11:65028627-65030620	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:65028915-65030658	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:65028325-65030623	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:65028341-65030737	SK-N-MC	brain:	n/a	n/a
11	SIN3AK20	chr11:65028700-65030384	MCF-7	breast:	n/a	n/a
12	MAX	chr11:65028630-65030636	A549	lung:	n/a	chr11:65028930-65028939
13	POLR2A	chr11:65028567-65030830	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr11:65028515-65030662	GM12892	blood:	n/a	n/a
15	PML	chr11:65028638-65030260	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:65028730-65030226	K562	blood:	n/a	n/a
17	POLR2A	chr11:65028487-65030611	K562	blood:	n/a	n/a
18	SPI1	chr11:65029690-65030256	HL-60	blood:	n/a	n/a
19	POLR2A	chr11:65030035-65030575	ECC-1	luminal epithelium:	n/a	n/a
20	MXI1	chr11:65028684-65030698	IMR90	lung:	n/a	n/a
21	POLR2A	chr11:65028513-65030656	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:65028493-65030671	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:65030182-65030417	GM12878	blood:	n/a	n/a
24	WRNIP1	chr11:65029973-65030532	GM12878	blood:	n/a	n/a
25	HEY1	chr11:65028977-65030648	K562	blood:	n/a	n/a
26	MXI1	chr11:65028528-65030727	SK-N-SH	brain:	n/a	n/a
27	SMARCC1	chr11:65029007-65030236	Hela-S3	cervix:	n/a	n/a
28	HA-E2F1	chr11:65028920-65030224	MCF-7	breast:	n/a	chr11:65029406-65029423 chr11:65029380-65029387 chr11:65029311-65029320 chr11:65029293-65029302 chr11:65029409-65029417 chr11:65029060-65029069 chr11:65029380-65029387 chr11:65029409-65029416 chr11:65029856-65029868 chr11:65029409-65029417 chr11:65029380-65029387 chr11:65029384-65029393
29	POLR2A	chr11:65028627-65030642	GM12892	blood:	n/a	n/a
30	CHD1	chr11:65030049-65030225	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:65028710-65030675	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr11:65028621-65030568	K562	blood:	n/a	n/a
33	RUNX3	chr11:65029971-65030658	GM12878	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65027906..65030927-chr11:65265746..65268595,3	K562	blood:
2	chr11:64947729..64951218-chr11:65027798..65031522,5	MCF-7	breast:
3	chr11:64884104..64886722-chr11:65028926..65030544,2	MCF-7	breast:
4	chr11:64900888..64904024-chr11:65027824..65031103,3	K562	blood:
5	chr11:64901495..64903969-chr11:65026515..65030932,5	MCF-7	breast:
6	chr11:65028103..65030991-chr11:65188788..65191974,4	K562	blood:
7	chr11:64946608..64950484-chr11:65027800..65030670,5	K562	blood:
8	chr11:64862784..64865189-chr11:65028595..65030936,2	K562	blood:
9	chr11:65029680..65031344-chr11:65031717..65033527,2	MCF-7	breast:
10	chr11:64948574..64950369-chr11:65028562..65030445,2	MCF-7	breast:
11	chr11:65028467..65031251-chr11:65099786..65102995,3	MCF-7	breast:
12	chr11:64947644..64950610-chr11:65027945..65030670,5	K562	blood:
13	chr11:64887057..64892358-chr11:65027493..65031887,5	K562	blood:
14	chr11:64883635..64887153-chr11:65027849..65031198,3	MCF-7	breast:
15	chr11:65029024..65031738-chr11:65081307..65084090,2	K562	blood:
16	chr11:65029710..65031446-chr11:65032712..65035703,3	K562	blood:
17	chr11:65029300..65032261-chr11:65099980..65102412,3	K562	blood:
18	chr11:64878321..64880931-chr11:65028635..65030509,3	MCF-7	breast:
19	chr11:65028603..65032064-chr11:65049175..65051003,3	MCF-7	breast:
20	chr11:65028586..65031401-chr11:65080311..65084684,5	MCF-7	breast:
21	chr11:65028264..65031673-chr11:65033494..65039309,8	MCF-7	breast:
22	chr11:64883613..64891269-chr11:65027573..65033885,11	K562	blood:
23	chr11:65027521..65031518-chr11:65033688..65038913,7	MCF-7	breast:
24	chr11:64880986..64883460-chr11:65027641..65030397,3	K562	blood:

No data

Variant related genes	Relation type
POLA2	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000149792	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10750761	0.81[ASN][1000 genomes]
rs1152611	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12269727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs28781278	0.89[AMR][1000 genomes]
rs2904966	1.00[CHB][hapmap]
rs2904967	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2904979	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2904980	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2904981	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904983	0.83[ASN][1000 genomes]
rs2904984	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957111	0.83[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3015999	0.87[ASN][1000 genomes]
rs3016000	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016001	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs482842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526502	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]
rs541829	0.80[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs560097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571128	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs603286	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs620427	1.00[CHB][hapmap]
rs625427	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630055	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[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	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap]
rs676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8638	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[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
rs592050	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs592050	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65028400-65030200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:65028400-65030400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr11:65028400-65030600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr11:65028400-65030800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:65028600-65030200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr11:65028600-65030200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:65028600-65030200	Active TSS	Fetal Kidney	kidney
8	chr11:65028600-65030400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:65028600-65030400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:65028600-65030400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr11:65028600-65030400	Active TSS	HSMMtube	muscle
12	chr11:65028600-65030600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:65028600-65030600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr11:65028600-65030800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:65028600-65030800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:65028800-65030200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr11:65028800-65030200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:65028800-65030200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:65028800-65030200	Active TSS	Aorta	Aorta
20	chr11:65028800-65030200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr11:65028800-65030200	Active TSS	Gastric	stomach
22	chr11:65028800-65030200	Active TSS	Left Ventricle	heart
23	chr11:65028800-65030200	Active TSS	Psoas Muscle	Psoas
24	chr11:65028800-65030400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:65028800-65030400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:65028800-65030400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:65028800-65030400	Active TSS	Esophagus	oesophagus
28	chr11:65028800-65030400	Active TSS	Fetal Muscle Trunk	muscle
29	chr11:65028800-65030400	Active TSS	Ovary	ovary
30	chr11:65028800-65030600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr11:65028800-65030600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:65028800-65030600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:65028800-65030600	Active TSS	Fetal Brain Female	brain
34	chr11:65028800-65030600	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr11:65028800-65030800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:65028800-65031400	Active TSS	GM12878-XiMat	blood
37	chr11:65029000-65030200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:65029000-65030200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr11:65029000-65030200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:65029000-65030200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr11:65029000-65030200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:65029000-65030200	Active TSS	Primary T cells from cord blood	blood
43	chr11:65029000-65030200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:65029000-65030200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr11:65029000-65030200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr11:65029000-65030200	Active TSS	Fetal Intestine Large	intestine
47	chr11:65029000-65030200	Active TSS	Fetal Lung	lung
48	chr11:65029000-65030200	Active TSS	Small Intestine	intestine
49	chr11:65029000-65030200	Active TSS	Stomach Mucosa	stomach
50	chr11:65029000-65030200	Active TSS	HMEC	breast

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