Variant report

Variant	rs854888
Chromosome Location	chr12:47469462-47469463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr12:47468630-47470193	A549	lung:	n/a	n/a
2	SIN3AK20	chr12:47468636-47470065	A549	lung:	n/a	n/a
3	MAX	chr12:47468669-47470079	A549	lung:	n/a	n/a
4	TCF12	chr12:47468604-47469653	A549	lung:	n/a	n/a
5	SIN3AK20	chr12:47468652-47470062	A549	lung:	n/a	n/a
6	SP1	chr12:47468688-47470189	A549	lung:	n/a	chr12:47469261-47469270
7	EP300	chr12:47468730-47470175	A549	lung:	n/a	chr12:47468761-47468771
8	BCL3	chr12:47468596-47470230	A549	lung:	n/a	n/a
9	POLR2A	chr12:47469155-47469521	A549	lung:	n/a	n/a
10	POLR2A	chr12:47469162-47469463	A549	lung:	n/a	n/a
11	JUND	chr12:47469039-47469921	A549	lung:	n/a	n/a
12	POLR2A	chr12:47468968-47469498	A549	lung:	n/a	n/a
13	PBX3	chr12:47468665-47469609	A549	lung:	n/a	n/a
14	PBX3	chr12:47468576-47470014	A549	lung:	n/a	n/a
15	GATA3	chr12:47468557-47470087	A549	lung:	n/a	n/a
16	REST	chr12:47468653-47470251	A549	lung:	n/a	n/a
17	REST	chr12:47469141-47469478	A549	lung:	n/a	n/a
18	FOSL2	chr12:47468529-47470332	A549	lung:	n/a	n/a
19	ELF1	chr12:47468667-47470016	A549	lung:	n/a	n/a
20	ZBTB33	chr12:47468633-47470149	A549	lung:	n/a	n/a
21	BCL3	chr12:47466534-47473485	A549	lung:	n/a	chr12:47473417-47473426 chr12:47473419-47473432
22	JUND	chr12:47468582-47470293	A549	lung:	n/a	n/a
23	USF1	chr12:47468549-47470132	A549	lung:	n/a	n/a
24	ETS1	chr12:47468837-47469571	A549	lung:	n/a	chr12:47469319-47469336
25	POLR2A	chr12:47468642-47470090	K562	blood:	n/a	n/a
26	POLR2A	chr12:47468540-47475394	A549	lung:	n/a	n/a
27	TCF12	chr12:47468475-47470222	A549	lung:	n/a	n/a
28	ZBTB33	chr12:47468879-47469718	A549	lung:	n/a	n/a
29	SIX5	chr12:47468477-47473570	A549	lung:	n/a	n/a
30	POLR2A	chr12:47469281-47469468	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:47468454..47471376-chr12:47472696..47475004,3	K562	blood:
2	chr12:47467597..47469569-chr12:47490059..47491619,2	MCF-7	breast:
3	chr12:47463342..47465286-chr12:47468931..47471873,3	K562	blood:
4	chr12:47417417..47420074-chr12:47466882..47469714,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCED1B	TF binding region
ENSG00000179715	Chromatin interaction
ENSG00000139211	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1101753	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854890	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv694	chr12:47460716-47473382	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47460400-47469600	Weak transcription	HSMM	muscle
2	chr12:47460800-47470400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:47460800-47471800	Weak transcription	Fetal Intestine Small	intestine
4	chr12:47461800-47470000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:47462600-47471400	Weak transcription	Lung	lung
6	chr12:47462800-47471200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:47463200-47469800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:47463200-47471400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:47463400-47472400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:47463800-47469800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:47464000-47469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:47464000-47471000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:47465200-47469600	Weak transcription	Aorta	Aorta
14	chr12:47465200-47471200	Weak transcription	Pancreas	Pancrea
15	chr12:47467400-47471000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:47468800-47469600	Genic enhancers	NH-A	brain
17	chr12:47468800-47472400	Weak transcription	HUVEC	blood vessel
18	chr12:47469000-47469800	Enhancers	Colon Smooth Muscle	Colon
19	chr12:47469000-47469800	Strong transcription	Ovary	ovary
20	chr12:47469000-47473200	Transcr. at gene 5' and 3'	A549	lung
21	chr12:47469200-47469600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr12:47469200-47469600	Enhancers	NHEK	skin
23	chr12:47469200-47470000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:47469400-47469600	Enhancers	HMEC	breast
25	chr12:47469400-47469800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:47469400-47470000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:47469400-47470000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:47469400-47472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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