Variant report

Variant	rs12292120
Chromosome Location	chr11:85780248-85780249
allele	C/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	FOXA1	chr11:85780003-85780425	HepG2	liver:	n/a	n/a
2	ATF2	chr11:85779976-85781265	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:85779909-85780271	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:85779896-85780680	PANC-1	pancreas:	n/a	n/a
5	CEBPB	chr11:85779930-85781270	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:85779907-85781256	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr11:85779354-85781130	Hela-S3	cervix:	n/a	chr11:85780166-85780175
8	MYC	chr11:85779999-85781060	MCF10A-Er-Src	breast:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
9	BHLHE40	chr11:85779942-85781147	HepG2	liver:	n/a	chr11:85780161-85780182 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780349-85780362 chr11:85780167-85780176 chr11:85780345-85780366 chr11:85780168-85780177 chr11:85780165-85780178 chr11:85780166-85780175 chr11:85780352-85780361 chr11:85780351-85780360
10	ATF2	chr11:85780180-85781254	GM12878	blood:	n/a	n/a
11	MYC	chr11:85780086-85780598	HepG2	liver:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780162-85780181 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
12	POLR2A	chr11:85779071-85781362	GM19099	blood:	n/a	n/a
13	CTCF	chr11:85780220-85780370	HCPEpiC	choroid plexus:	n/a	n/a
14	TBP	chr11:85778736-85781124	K562	blood:	n/a	n/a
15	RELA	chr11:85779379-85781165	GM12891	blood:	n/a	n/a
16	YY1	chr11:85779913-85780365	HepG2	liver:	n/a	chr11:85780153-85780164 chr11:85780107-85780129 chr11:85780269-85780283 chr11:85780119-85780129 chr11:85780119-85780129 chr11:85780269-85780278
17	YY1	chr11:85779899-85780269	A549	lung:	n/a	chr11:85780153-85780164 chr11:85780107-85780129 chr11:85780119-85780129 chr11:85780119-85780129
18	USF1	chr11:85779974-85780558	A549	lung:	n/a	chr11:85780161-85780182 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780349-85780362 chr11:85780167-85780176 chr11:85780345-85780366 chr11:85780168-85780177 chr11:85780165-85780178 chr11:85780166-85780175 chr11:85780352-85780361 chr11:85780351-85780360
19	EP300	chr11:85779846-85780508	T-47D	breast:	n/a	chr11:85780271-85780280
20	STAT3	chr11:85780083-85781253	MCF10A-Er-Src	breast:	n/a	n/a
21	MAZ	chr11:85778173-85781166	K562	blood:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
22	TAF1	chr11:85779889-85781074	SK-N-SH	brain:	n/a	n/a
23	TEAD4	chr11:85779810-85781266	ECC-1	luminal epithelium:	n/a	n/a
24	USF1	chr11:85779838-85781131	SK-N-SH	brain:	n/a	chr11:85780161-85780182 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780349-85780362 chr11:85780167-85780176 chr11:85779853-85779869 chr11:85780345-85780366 chr11:85780168-85780177 chr11:85780165-85780178 chr11:85780166-85780175 chr11:85780352-85780361 chr11:85780351-85780360
25	NR3C1	chr11:85779776-85780573	A549	lung:	n/a	n/a
26	SIN3AK20	chr11:85779644-85780281	PANC-1	pancreas:	n/a	n/a
27	TAF1	chr11:85779045-85781169	H1-hESC	embryonic stem cell:	n/a	n/a
28	PBX3	chr11:85779790-85781881	SK-N-SH	brain:	n/a	chr11:85781807-85781816 chr11:85781678-85781689
29	STAT1	chr11:85779983-85781162	GM12878	blood:	n/a	chr11:85780033-85780045 chr11:85780060-85780072
30	CREB1	chr11:85779787-85781174	K562	blood:	n/a	n/a
31	SIN3A	chr11:85778528-85781121	H1-hESC	embryonic stem cell:	n/a	chr11:85780166-85780175 chr11:85779848-85779859 chr11:85780168-85780177 chr11:85780352-85780361
32	FOSL2	chr11:85779954-85780489	HepG2	liver:	n/a	n/a
33	SP1	chr11:85779905-85781207	GM12878	blood:	n/a	chr11:85781125-85781146 chr11:85779912-85779926 chr11:85779911-85779925
34	GTF2F1	chr11:85779994-85780769	H1-hESC	embryonic stem cell:	n/a	n/a
35	NR2F2	chr11:85779905-85781210	K562	blood:	n/a	n/a
36	GATA3	chr11:85779884-85780597	T-47D	breast:	n/a	n/a
37	EBF1	chr11:85780017-85781134	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:85779060-85780458	K562	blood:	n/a	n/a
39	EP300	chr11:85779994-85781312	GM12878	blood:	n/a	chr11:85780271-85780280 chr11:85781025-85781039 chr11:85781026-85781035
40	YY1	chr11:85779891-85780747	ECC-1	luminal epithelium:	n/a	chr11:85780153-85780164 chr11:85780107-85780129 chr11:85780269-85780283 chr11:85780119-85780129 chr11:85780119-85780129 chr11:85780269-85780278
41	HDAC2	chr11:85779891-85780314	HepG2	liver:	n/a	chr11:85780274-85780283
42	STAT3	chr11:85780116-85780315	MCF10A-Er-Src	breast:	n/a	n/a
43	ZNF143	chr11:85779909-85781401	GM12878	blood:	n/a	chr11:85780270-85780280
44	YY1	chr11:85779869-85780671	HCT-116	colon:	n/a	chr11:85780153-85780164 chr11:85780107-85780129 chr11:85780269-85780283 chr11:85780119-85780129 chr11:85780119-85780129 chr11:85780269-85780278
45	NFIC	chr11:85779905-85780280	HepG2	liver:	n/a	n/a
46	YY1	chr11:85779724-85780577	H1-hESC	embryonic stem cell:	n/a	chr11:85780153-85780164 chr11:85780107-85780129 chr11:85780269-85780283 chr11:85780119-85780129 chr11:85780119-85780129 chr11:85780269-85780278
47	HDAC2	chr11:85780032-85780450	H1-hESC	embryonic stem cell:	n/a	chr11:85780274-85780283
48	FOXA1	chr11:85779951-85781149	T-47D	breast:	n/a	n/a
49	NFYB	chr11:85780047-85781363	GM12878	blood:	n/a	n/a
50	POLR2A	chr11:85775966-85781389	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85777862..85782517-chr11:85902953..85907117,7	K562	blood:
2	chr11:85779917..85781059-chr11:85904304..85905143,3	K562	blood:
3	chr1:149783817..149784624-chr11:85780019..85780945,2	HCT-116	colon:
4	chr1:160990808..160991668-chr11:85780243..85780839,2	HCT-116	colon:
5	chr11:85779554..85782905-chr11:85860304..85865248,6	K562	blood:
6	chr11:85778609..85781292-chr11:85954393..85956232,2	K562	blood:
7	chr11:85778910..85781849-chr11:85954546..85957728,3	K562	blood:
8	chr11:85779691..85780554-chr5:40834970..40835897,2	Hela-S3	cervix:
9	chr11:85779839..85780644-chr16:50099773..50100446,2	NB4	blood:
10	chr11:85776467..85780584-chr11:85902948..85906650,5	MCF-7	breast:
11	chr11:85779754..85780343-chr13:111367026..111368006,2	Hela-S3	cervix:
12	chr11:85780118..85780978-chr12:21590354..21590877,2	Hela-S3	cervix:
13	chr11:85520681..85523600-chr11:85778386..85780657,2	MCF-7	breast:
14	chr11:85375979..85377499-chr11:85779750..85781435,2	K562	blood:

Variant related genes	Relation type
PICALM	TF binding region
ENSG00000145592	Chromatin interaction
ENSG00000259843	Chromatin interaction
ENSG00000155393	Chromatin interaction
ENSG00000254502	Chromatin interaction
ENSG00000074266	Chromatin interaction
ENSG00000203814	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000200877	Chromatin interaction
ENSG00000121350	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000254699	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11234525	1.00[AMR][1000 genomes]
rs12279581	1.00[AMR][1000 genomes]
rs12288262	0.83[AFR][1000 genomes]

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	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 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	chr11:85773600-85781000	Active TSS	Right Ventricle	heart
2	chr11:85773800-85780600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr11:85773800-85780600	Active TSS	GM12878-XiMat	blood
4	chr11:85775000-85780600	Active TSS	Stomach Smooth Muscle	stomach
5	chr11:85775600-85780800	Active TSS	Ovary	ovary
6	chr11:85775600-85781000	Active TSS	Hela-S3	cervix
7	chr11:85775800-85780600	Active TSS	HSMMtube	muscle
8	chr11:85776000-85781200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:85776200-85780600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:85776200-85780600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:85776200-85780800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:85776200-85780800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:85776400-85780600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:85776400-85780600	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr11:85776400-85780600	Active TSS	HMEC	breast
16	chr11:85776400-85780800	Active TSS	Right Atrium	heart
17	chr11:85776400-85781000	Active TSS	HSMM	muscle
18	chr11:85776400-85781000	Active TSS	NHLF	lung
19	chr11:85776400-85781200	Active TSS	Psoas Muscle	Psoas
20	chr11:85776600-85780400	Active TSS	Primary T cells fromperipheralblood	blood
21	chr11:85776600-85780400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:85776600-85780400	Active TSS	Fetal Muscle Leg	muscle
23	chr11:85776600-85780800	Active TSS	Aorta	Aorta
24	chr11:85776600-85781000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr11:85776800-85780600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:85776800-85780600	Active TSS	Brain Substantia Nigra	brain
27	chr11:85776800-85780600	Active TSS	Thymus	Thymus
28	chr11:85776800-85780600	Active TSS	NHEK	skin
29	chr11:85776800-85780800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:85776800-85780800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:85776800-85780800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:85776800-85781000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:85777000-85780400	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr11:85777000-85780600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr11:85777000-85780600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:85777000-85780600	Active TSS	Fetal Intestine Large	intestine
37	chr11:85777000-85780600	Active TSS	Fetal Intestine Small	intestine
38	chr11:85777000-85780600	Active TSS	Placenta	Placenta
39	chr11:85777000-85780600	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr11:85777000-85780600	Active TSS	NH-A	brain
41	chr11:85777000-85780600	Active TSS	NHDF-Ad	bronchial
42	chr11:85777000-85780800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr11:85777000-85781000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr11:85777200-85780600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr11:85777200-85780600	Active TSS	Fetal Stomach	stomach
46	chr11:85777200-85780600	Active TSS	Fetal Thymus	thymus
47	chr11:85777200-85780600	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr11:85777200-85780600	Active TSS	HUVEC	blood vessel
49	chr11:85777200-85780600	Active TSS	K562	blood
50	chr11:85777200-85780800	Active TSS	Liver	Liver

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