Variant report

Variant	rs12792817
Chromosome Location	chr11:45202450-45202451
allele	C/G
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	POLR2A	chr11:45201038-45203556	Hela-S3	cervix:	n/a	n/a
2	GATA1	chr11:45202288-45202761	PBDE	blood:	n/a	chr11:45202564-45202573
3	POLR2A	chr11:45201832-45203358	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:45202248-45202806	PANC-1	pancreas:	n/a	n/a
5	MAZ	chr11:45201260-45203091	Hela-S3	cervix:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
6	POLR2A	chr11:45201901-45202865	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr11:45202417-45202684	MCF10A-Er-Src	breast:	n/a	chr11:45202435-45202445
8	RFX5	chr11:45202380-45202830	Hela-S3	cervix:	n/a	n/a
9	BHLHE40	chr11:45202346-45202654	K562	blood:	n/a	n/a
10	POLR2A	chr11:45201840-45202822	IMR90	lung:	n/a	n/a
11	POLR2A	chr11:45201669-45202950	Hela-S3	cervix:	n/a	n/a
12	JUN	chr11:45202404-45202896	K562	blood:	n/a	chr11:45202563-45202572
13	HA-E2F1	chr11:45201670-45202928	Hela-S3	cervix:	n/a	chr11:45201841-45201851 chr11:45202410-45202419 chr11:45202132-45202141 chr11:45202479-45202489
14	TCF7L2	chr11:45201567-45202918	HCT-116	colon:	n/a	n/a
15	ELK1	chr11:45202425-45202768	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr11:45202372-45202792	Hela-S3	cervix:	n/a	n/a
17	MAX	chr11:45202368-45202871	SK-N-SH	brain:	n/a	chr11:45202435-45202445 chr11:45202681-45202691
18	POLR2A	chr11:45201729-45202799	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr11:45201655-45202731	MCF-7	breast:	n/a	n/a
20	POLR2A	chr11:45201346-45202987	PBDE	blood:	n/a	n/a
21	ZBTB7A	chr11:45201247-45203155	ECC-1	luminal epithelium:	n/a	chr11:45202789-45202798
22	POLR2A	chr11:45201611-45202761	ECC-1	luminal epithelium:	n/a	n/a
23	ZBTB7A	chr11:45201489-45203332	ECC-1	luminal epithelium:	n/a	chr11:45202789-45202798
24	MAX	chr11:45201156-45203056	A549	lung:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
25	POLR2A	chr11:45202370-45203153	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr11:45202193-45202646	PANC-1	pancreas:	n/a	n/a
27	E2F6	chr11:45202421-45202774	A549	lung:	n/a	chr11:45202479-45202489
28	E2F6	chr11:45202380-45202938	A549	lung:	n/a	chr11:45202410-45202419 chr11:45202479-45202489
29	MYC	chr11:45201608-45202926	Hela-S3	cervix:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
30	NFIC	chr11:45201448-45202774	ECC-1	luminal epithelium:	n/a	n/a
31	EP300	chr11:45201322-45202864	ECC-1	luminal epithelium:	n/a	chr11:45202481-45202490 chr11:45202467-45202483 chr11:45202479-45202488
32	TCF12	chr11:45201361-45202942	ECC-1	luminal epithelium:	n/a	chr11:45201861-45201868 chr11:45202040-45202048 chr11:45201471-45201481
33	HDAC2	chr11:45202311-45202540	HepG2	liver:	n/a	n/a
34	BHLHE40	chr11:45202348-45202626	HepG2	liver:	n/a	n/a
35	FOSL2	chr11:45202351-45202753	A549	lung:	n/a	chr11:45202563-45202572
36	SIN3A	chr11:45202379-45202640	H1-hESC	embryonic stem cell:	n/a	n/a
37	TEAD4	chr11:45201456-45202826	ECC-1	luminal epithelium:	n/a	n/a
38	ZNF143	chr11:45201537-45202833	Hela-S3	cervix:	n/a	chr11:45202480-45202490 chr11:45202119-45202137 chr11:45202787-45202797
39	TCF7L2	chr11:45202401-45202921	Hela-S3	cervix:	n/a	n/a
40	MAX	chr11:45201530-45202884	ECC-1	luminal epithelium:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
41	EP300	chr11:45201716-45202861	SK-N-SH	brain:	n/a	chr11:45202481-45202490 chr11:45202467-45202483 chr11:45202479-45202488
42	TAF1	chr11:45202392-45202590	H1-hESC	embryonic stem cell:	n/a	n/a
43	HCFC1	chr11:45200158-45203524	Hela-S3	cervix:	n/a	n/a
44	MAX	chr11:45201635-45202704	H1-hESC	embryonic stem cell:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
45	POLR2A	chr11:45201075-45203095	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr11:45201711-45202934	A549	lung:	n/a	n/a
47	POLR2A	chr11:45201810-45203261	HepG2	liver:	n/a	n/a
48	POLR2A	chr11:45202117-45202838	HUVEC	blood vessel:	n/a	n/a
49	JUND	chr11:45202397-45202654	H1-hESC	embryonic stem cell:	n/a	chr11:45202561-45202572 chr11:45202563-45202572
50	TCF12	chr11:45201588-45202902	A549	lung:	n/a	chr11:45201861-45201868 chr11:45202040-45202048

No.	Distal block	Cell Line	Cell type
1	chr11:45200855..45203126-chr11:45215617..45218451,2	MCF-7	breast:
2	chr11:45202128..45202855-chr20:42839088..42839664,2	Hela-S3	cervix:
3	chr11:45200307..45202663-chr11:45284381..45286142,2	MCF-7	breast:
4	chr1:45805524..45806078-chr11:45202033..45202587,2	Hela-S3	cervix:
5	chr11:45192972..45194599-chr11:45201172..45203381,2	MCF-7	breast:
6	chr11:45175116..45179672-chr11:45200428..45203177,5	MCF-7	breast:
7	chr11:45184562..45186695-chr11:45200479..45203077,3	MCF-7	breast:
8	chr11:45201839..45203061-chr11:62608513..62609201,3	Hela-S3	cervix:
9	chr11:45197003..45199885-chr11:45200062..45203295,4	MCF-7	breast:
10	chr11:45164160..45171283-chr11:45198764..45207868,26	MCF-7	breast:
11	chr11:45167893..45171206-chr11:45200303..45204446,5	MCF-7	breast:
12	chr11:45194753..45196374-chr11:45201257..45203053,2	K562	blood:
13	chr11:45184515..45187339-chr11:45200209..45203185,3	MCF-7	breast:
14	chr11:45198038..45200722-chr11:45201190..45202692,2	MCF-7	breast:
15	chr1:20834026..20834793-chr11:45201916..45202662,2	Hela-S3	cervix:
16	chr11:45201835..45202455-chr17:27620880..27621538,2	Hela-S3	cervix:
17	chr11:45201511..45203799-chr11:45256779..45259525,2	MCF-7	breast:

Variant related genes	Relation type
PRDM11	TF binding region
ENSG00000132773	Chromatin interaction
ENSG00000019485	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000090432	Chromatin interaction
ENSG00000254664	Chromatin interaction
ENSG00000132823	Chromatin interaction
ENSG00000223891	Chromatin interaction
ENSG00000108256	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3758729	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	esv3406728	chr11:45201001-45203549	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3326620	chr11:45201401-45203949	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12792817	PRDM11	cis	Thyroid	GTEx
rs12792817	SYT13	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45201400-45202600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:45201400-45203000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:45201400-45203000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:45201400-45203000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:45201400-45203400	Flanking Active TSS	Colonic Mucosa	Colon
6	chr11:45201400-45203400	Enhancers	Fetal Brain Male	brain
7	chr11:45201600-45202600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:45201600-45202800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:45201600-45203000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:45201600-45203000	Active TSS	Brain Angular Gyrus	brain
11	chr11:45201600-45203000	Active TSS	HepG2	liver
12	chr11:45201600-45203600	Active TSS	Aorta	Aorta
13	chr11:45201800-45202600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr11:45201800-45202600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:45201800-45202600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:45201800-45202600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr11:45201800-45202600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:45201800-45202600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr11:45201800-45202600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:45201800-45202600	Active TSS	Brain Cingulate Gyrus	brain
21	chr11:45201800-45202600	Active TSS	Brain Hippocampus Middle	brain
22	chr11:45201800-45202600	Active TSS	Brain Substantia Nigra	brain
23	chr11:45201800-45202600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr11:45201800-45202600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr11:45201800-45202600	Active TSS	Fetal Intestine Small	intestine
26	chr11:45201800-45202600	Enhancers	Fetal Lung	lung
27	chr11:45201800-45202600	Active TSS	Lung	lung
28	chr11:45201800-45202600	Active TSS	Ovary	ovary
29	chr11:45201800-45202600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr11:45201800-45202600	Active TSS	Rectal Smooth Muscle	rectum
31	chr11:45201800-45202600	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr11:45201800-45202600	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr11:45201800-45202600	Active TSS	Osteobl	bone
34	chr11:45201800-45202800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:45201800-45202800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr11:45201800-45202800	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr11:45201800-45202800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:45201800-45202800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:45201800-45202800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr11:45201800-45202800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:45201800-45202800	Active TSS	Colon Smooth Muscle	Colon
42	chr11:45201800-45202800	Active TSS	Duodenum Mucosa	Duodenum
43	chr11:45201800-45202800	Active TSS	Fetal Brain Female	brain
44	chr11:45201800-45202800	Active TSS	Fetal Intestine Large	intestine
45	chr11:45201800-45202800	Weak transcription	Fetal Kidney	kidney
46	chr11:45201800-45202800	Active TSS	Fetal Stomach	stomach
47	chr11:45201800-45202800	Active TSS	Left Ventricle	heart
48	chr11:45201800-45202800	Bivalent/Poised TSS	Thymus	Thymus
49	chr11:45201800-45202800	Active TSS	A549	lung
50	chr11:45201800-45202800	Active TSS	Hela-S3	cervix

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