Variant report

Variant	rs12227040
Chromosome Location	chr12:56481118-56481119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56481063-56481237	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr12:56481102-56481238	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:56480065-56483649	HepG2	liver:	n/a	n/a
4	FOXA2	chr12:56481035-56481490	A549	lung:	n/a	n/a
5	CTCF	chr12:56481080-56481230	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:56480928-56481378	MCF-7	breast:	n/a	n/a
7	FOXA1	chr12:56481022-56481391	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:56481003-56481197	HepG2	liver:	n/a	n/a
9	HEY1	chr12:56480838-56481226	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:56480899-56481398	HepG2	liver:	n/a	n/a
11	CTCF	chr12:56481080-56481230	Caco-2	colon:	n/a	n/a
12	FOXA2	chr12:56480992-56481391	A549	lung:	n/a	n/a
13	EGR1	chr12:56481050-56481285	K562	blood:	n/a	n/a
14	YY1	chr12:56481001-56481318	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:56480940-56482549	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:56480932-56481301	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:56480932-56482730	HepG2	liver:	n/a	n/a
18	FOXA1	chr12:56480962-56481357	T-47D	breast:	n/a	n/a
19	FOXA2	chr12:56481094-56481260	HepG2	liver:	n/a	n/a
20	FOXA1	chr12:56480901-56481431	T-47D	breast:	n/a	n/a
21	FOXA1	chr12:56480931-56481278	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56435284..56441183-chr12:56476886..56481327,8	MCF-7	breast:
2	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
3	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
4	chr12:56475587..56477681-chr12:56479959..56483381,3	K562	blood:
5	chr12:56479547..56482391-chr12:56486376..56489009,4	MCF-7	breast:
6	chr12:56480457..56482671-chr12:56551431..56553649,2	MCF-7	breast:
7	chr12:56472197..56476808-chr12:56477200..56483474,8	K562	blood:
8	chr12:56434874..56437408-chr12:56478548..56481298,5	MCF-7	breast:
9	chr12:56480948..56483944-chr12:56582412..56584224,2	MCF-7	breast:
10	chr12:56477785..56480732-chr12:56480999..56482535,2	K562	blood:

No data

Variant related genes	Relation type
ERBB3	TF binding region
ENSG00000197728	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000257411	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11171746	1.00[GIH][hapmap]
rs11504023	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12296387	1.00[GIH][hapmap]
rs12309692	1.00[GIH][hapmap]
rs34102859	1.00[MEX][hapmap]
rs35807059	1.00[MEX][hapmap]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56474400-56497200	Weak transcription	Right Atrium	heart
2	chr12:56475000-56485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:56475800-56482400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:56476000-56481800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:56476200-56497200	Weak transcription	Fetal Kidney	kidney
6	chr12:56476400-56483200	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr12:56476600-56487400	Weak transcription	Lung	lung
8	chr12:56476600-56496400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:56476600-56497600	Weak transcription	Small Intestine	intestine
10	chr12:56476800-56487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:56477000-56497000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:56477000-56497000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:56477200-56481600	Genic enhancers	Rectal Mucosa Donor 31	rectum
14	chr12:56477600-56496600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:56477800-56481400	Genic enhancers	Duodenum Mucosa	Duodenum
16	chr12:56477800-56481600	Genic enhancers	Liver	Liver
17	chr12:56477800-56481600	Genic enhancers	Rectal Mucosa Donor 29	rectum
18	chr12:56477800-56485800	Strong transcription	Fetal Stomach	stomach
19	chr12:56477800-56496200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr12:56478600-56496400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:56478800-56481800	Genic enhancers	Brain Substantia Nigra	brain
22	chr12:56478800-56482400	Enhancers	K562	blood
23	chr12:56478800-56483000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:56479000-56481200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:56479200-56486400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:56479200-56486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:56479200-56489800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:56479200-56496000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:56479200-56496400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:56479400-56496800	Strong transcription	Fetal Intestine Small	intestine
31	chr12:56479400-56497200	Strong transcription	Fetal Intestine Large	intestine
32	chr12:56479800-56481200	Enhancers	Colonic Mucosa	Colon
33	chr12:56479800-56481200	Genic enhancers	HSMMtube	muscle
34	chr12:56479800-56481600	Genic enhancers	Fetal Muscle Leg	muscle
35	chr12:56480000-56481200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:56480000-56481200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:56480000-56481200	Genic enhancers	Brain Hippocampus Middle	brain
38	chr12:56480000-56481200	Enhancers	Fetal Heart	heart
39	chr12:56480000-56481600	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr12:56480000-56481600	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr12:56480000-56481600	Genic enhancers	Placenta	Placenta
42	chr12:56480000-56481800	Genic enhancers	Pancreas	Pancrea
43	chr12:56480000-56495800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:56480000-56496400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:56480200-56481200	Enhancers	Brain Angular Gyrus	brain
46	chr12:56480200-56481200	Enhancers	Hela-S3	cervix
47	chr12:56480200-56482000	Genic enhancers	Stomach Mucosa	stomach
48	chr12:56480200-56483200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:56480200-56483200	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr12:56480400-56481200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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