Variant report

Variant	rs41544519
Chromosome Location	chr11:65029369-65029370
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr11:65028968-65029626	H1-hESC	embryonic stem cell:	n/a	chr11:65029310-65029321 chr11:65029061-65029070 chr11:65029380-65029394 chr11:65029059-65029070 chr11:65029307-65029321 chr11:65029289-65029303 chr11:65029383-65029392 chr11:65029310-65029321 chr11:65029292-65029301 chr11:65029258-65029272 chr11:65029292-65029306 chr11:65029383-65029394 chr11:65029312-65029321 chr11:65029291-65029302 chr11:65029258-65029269 chr11:65029059-65029073 chr11:65029292-65029303
2	SIN3AK20	chr11:65029336-65029710	PANC-1	pancreas:	n/a	n/a
3	MYC	chr11:65029035-65029430	MCF-7	breast:	n/a	n/a
4	E2F6	chr11:65028833-65030163	A549	lung:	n/a	chr11:65029406-65029423 chr11:65029380-65029387 chr11:65029408-65029416 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
5	TRIM28	chr11:65028875-65029643	K562	blood:	n/a	n/a
6	ATF2	chr11:65028769-65029690	GM12878	blood:	n/a	n/a
7	BCL3	chr11:65028869-65029934	A549	lung:	n/a	n/a
8	SIN3A	chr11:65028947-65029796	GM12878	blood:	n/a	n/a
9	EP300	chr11:65029113-65029610	GM12878	blood:	n/a	n/a
10	MAZ	chr11:65029063-65029893	K562	blood:	n/a	n/a
11	POLR2A	chr11:65022945-65033166	K562	blood:	n/a	n/a
12	MAX	chr11:65028909-65029994	Hela-S3	cervix:	n/a	chr11:65028930-65028939
13	POLR2A	chr11:65029040-65029637	HUVEC	blood vessel:	n/a	n/a
14	ZKSCAN1	chr11:65028893-65029491	Hela-S3	cervix:	n/a	n/a
15	BHLHE40	chr11:65028935-65029620	K562	blood:	n/a	chr11:65029234-65029250
16	TAF1	chr11:65029009-65029626	GM12892	blood:	n/a	n/a
17	MTA3	chr11:65028405-65030309	GM12878	blood:	n/a	n/a
18	SMC3	chr11:65029040-65029946	Hela-S3	cervix:	n/a	chr11:65029742-65029752
19	POLR2A	chr11:65028686-65030050	K562	blood:	n/a	n/a
20	GATA3	chr11:65028707-65029437	T-47D	breast:	n/a	chr11:65029135-65029146
21	BRCA1	chr11:65029215-65029490	HepG2	liver:	n/a	n/a
22	TAF1	chr11:65028992-65029629	SK-N-SH	brain:	n/a	n/a
23	RCOR1	chr11:65028721-65029610	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr11:65028653-65029702	U87	brain:	n/a	n/a
25	ELF1	chr11:65029091-65029519	HepG2	liver:	n/a	n/a
26	EGR1	chr11:65029019-65029537	H1-hESC	embryonic stem cell:	n/a	chr11:65029273-65029283 chr11:65029384-65029393 chr11:65029312-65029321 chr11:65029293-65029302 chr11:65029259-65029268 chr11:65029260-65029269 chr11:65029311-65029320
27	USF1	chr11:65029122-65029479	SK-N-SH_RA	brain:	n/a	chr11:65029234-65029250
28	POLR2A	chr11:65028847-65030022	GM12878	blood:	n/a	n/a
29	JUND	chr11:65028972-65029632	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr11:65029004-65029841	ECC-1	luminal epithelium:	n/a	chr11:65029738-65029749 chr11:65029724-65029738
31	CEBPD	chr11:65029036-65029588	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:65028664-65030136	GM12892	blood:	n/a	n/a
33	MAFK	chr11:65029151-65029476	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr11:65029116-65029468	MCF10A-Er-Src	breast:	n/a	n/a
35	SIN3AK20	chr11:65029217-65029675	PFSK-1	brain:	n/a	n/a
36	ZNF143	chr11:65029093-65029484	GM12878	blood:	n/a	n/a
37	RXRA	chr11:65029028-65029526	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:65028963-65029911	GM18951	blood:	n/a	n/a
39	POLR2A	chr11:65028462-65030289	MCF-7	breast:	n/a	n/a
40	POLR2A	chr11:65028898-65029865	GM12891	blood:	n/a	n/a
41	ELF1	chr11:65028928-65029638	MCF-7	breast:	n/a	n/a
42	POLR2A	chr11:65028808-65030063	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr11:65028662-65029931	U87	brain:	n/a	n/a
44	FOXM1	chr11:65028873-65029761	GM12878	blood:	n/a	n/a
45	NFYB	chr11:65029073-65029566	GM12878	blood:	n/a	n/a
46	RELA	chr11:65028902-65029621	GM19099	blood:	n/a	n/a
47	POLR2A	chr11:65028984-65029879	GM15510	blood:	n/a	n/a
48	ZNF263	chr11:65029232-65030539	HEK293-T-REx	kidney:	n/a	chr11:65030227-65030236
49	NRF1	chr11:65029010-65029521	K562	blood:	n/a	chr11:65029310-65029321 chr11:65029061-65029070 chr11:65029380-65029394 chr11:65029059-65029070 chr11:65029307-65029321 chr11:65029289-65029303 chr11:65029383-65029392 chr11:65029310-65029321 chr11:65029292-65029301 chr11:65029258-65029272 chr11:65029292-65029306 chr11:65029383-65029394 chr11:65029312-65029321 chr11:65029291-65029302 chr11:65029258-65029269 chr11:65029059-65029073 chr11:65029292-65029303
50	MAX	chr11:65028844-65029987	H1-hESC	embryonic stem cell:	n/a	chr11:65028930-65028939

No.	Distal block	Cell Line	Cell type
1	chr11:65027906..65030927-chr11:65265746..65268595,3	K562	blood:
2	chr11:64654051..64656585-chr11:65027295..65030024,2	K562	blood:
3	chr11:65029282..65029828-chr9:131643733..131644465,2	Hela-S3	cervix:
4	chr11:64947729..64951218-chr11:65027798..65031522,5	MCF-7	breast:
5	chr11:64884104..64886722-chr11:65028926..65030544,2	MCF-7	breast:
6	chr11:64900888..64904024-chr11:65027824..65031103,3	K562	blood:
7	chr11:64901495..64903969-chr11:65026515..65030932,5	MCF-7	breast:
8	chr11:65028103..65030991-chr11:65188788..65191974,4	K562	blood:
9	chr11:64946608..64950484-chr11:65027800..65030670,5	K562	blood:
10	chr11:64862784..64865189-chr11:65028595..65030936,2	K562	blood:
11	chr11:64948574..64950369-chr11:65028562..65030445,2	MCF-7	breast:
12	chr11:65028467..65031251-chr11:65099786..65102995,3	MCF-7	breast:
13	chr11:64947644..64950610-chr11:65027945..65030670,5	K562	blood:
14	chr11:64887057..64892358-chr11:65027493..65031887,5	K562	blood:
15	chr11:64883635..64887153-chr11:65027849..65031198,3	MCF-7	breast:
16	chr11:65029024..65031738-chr11:65081307..65084090,2	K562	blood:
17	chr1:149858398..149859139-chr11:65029009..65029670,2	HCT-116	colon:
18	chr11:65029300..65032261-chr11:65099980..65102412,3	K562	blood:
19	chr11:64878321..64880931-chr11:65028635..65030509,3	MCF-7	breast:
20	chr11:64887534..64891326-chr11:65027495..65030120,4	MCF-7	breast:
21	chr11:65028603..65032064-chr11:65049175..65051003,3	MCF-7	breast:
22	chr11:65029007..65029854-chr6:70506100..70507044,2	Hela-S3	cervix:
23	chr11:65028586..65031401-chr11:65080311..65084684,5	MCF-7	breast:
24	chr11:65028772..65029575-chr18:44497156..44497741,2	NB4	blood:
25	chr11:65028264..65031673-chr11:65033494..65039309,8	MCF-7	breast:
26	chr11:64883613..64891269-chr11:65027573..65033885,11	K562	blood:
27	chr11:65027521..65031518-chr11:65033688..65038913,7	MCF-7	breast:
28	chr11:65029357..65029875-chr5:108083281..108083886,2	Hela-S3	cervix:
29	chr11:64880986..64883460-chr11:65027641..65030397,3	K562	blood:
30	chr11:65027939..65030134-chr11:65081779..65083802,2	MCF-7	breast:
31	chr11:64901151..64904024-chr11:65027824..65029855,2	K562	blood:

Variant related genes	Relation type
POLA2	TF binding region
ENSG00000167216	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000168216	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000151422	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000171097	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000136802	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000078043	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000014138	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11819804	0.83[AFR][1000 genomes]
rs11821851	0.85[AFR][1000 genomes]
rs11824738	0.83[AFR][1000 genomes]
rs35225270	0.81[AFR][1000 genomes]
rs41556122	0.85[AFR][1000 genomes]
rs7107815	0.92[AFR][1000 genomes]
rs7108941	0.85[AFR][1000 genomes]
rs7114046	0.92[AFR][1000 genomes]
rs7123885	0.92[AFR][1000 genomes]
rs7926687	0.92[AFR][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

No data

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	chr11:65028600-65029400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:65028600-65030000	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr11:65028600-65030000	Active TSS	NHLF	lung
8	chr11:65028600-65030200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr11:65028600-65030200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr11:65028600-65030200	Active TSS	Fetal Kidney	kidney
11	chr11:65028600-65030400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr11:65028600-65030400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:65028600-65030400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr11:65028600-65030400	Active TSS	HSMMtube	muscle
15	chr11:65028600-65030600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:65028600-65030600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr11:65028600-65030800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:65028600-65030800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:65028800-65030200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr11:65028800-65030200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:65028800-65030200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:65028800-65030200	Active TSS	Aorta	Aorta
23	chr11:65028800-65030200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr11:65028800-65030200	Active TSS	Gastric	stomach
25	chr11:65028800-65030200	Active TSS	Left Ventricle	heart
26	chr11:65028800-65030200	Active TSS	Psoas Muscle	Psoas
27	chr11:65028800-65030400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:65028800-65030400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:65028800-65030400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:65028800-65030400	Active TSS	Esophagus	oesophagus
31	chr11:65028800-65030400	Active TSS	Fetal Muscle Trunk	muscle
32	chr11:65028800-65030400	Active TSS	Ovary	ovary
33	chr11:65028800-65030600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr11:65028800-65030600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:65028800-65030600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:65028800-65030600	Active TSS	Fetal Brain Female	brain
37	chr11:65028800-65030600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr11:65028800-65030800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:65028800-65031400	Active TSS	GM12878-XiMat	blood
40	chr11:65029000-65029400	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr11:65029000-65029400	Active TSS	Primary B cells from peripheral blood	blood
42	chr11:65029000-65029600	Active TSS	Brain Germinal Matrix	brain
43	chr11:65029000-65029600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr11:65029000-65029600	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr11:65029000-65029800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:65029000-65029800	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr11:65029000-65029800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr11:65029000-65029800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:65029000-65029800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:65029000-65029800	Active TSS	Brain Hippocampus Middle	brain

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