Variant report

Variant	rs72884627
Chromosome Location	chr2:47629921-47629922
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	MAX	chr2:47629764-47630931	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:47629871-47630797	MCF-7	breast:	n/a	n/a
3	JUND	chr2:47629850-47630505	A549	lung:	n/a	chr2:47630259-47630268
4	SIN3AK20	chr2:47629888-47630734	HepG2	liver:	n/a	n/a
5	MAFK	chr2:47629885-47630435	Hela-S3	cervix:	n/a	n/a
6	RUNX3	chr2:47629200-47630855	GM12878	blood:	n/a	n/a
7	PBX3	chr2:47629730-47630953	A549	lung:	n/a	n/a
8	RAD21	chr2:47629851-47630164	H1-hESC	embryonic stem cell:	n/a	chr2:47629977-47629986 chr2:47629973-47629992 chr2:47629968-47629987
9	CEBPB	chr2:47629659-47630378	H1-hESC	embryonic stem cell:	n/a	n/a
10	ELF1	chr2:47629914-47630766	K562	blood:	n/a	chr2:47630225-47630237 chr2:47630715-47630727
11	POLR2A	chr2:47629785-47631345	K562	blood:	n/a	n/a
12	MAX	chr2:47629614-47631283	K562	blood:	n/a	n/a
13	POLR2A	chr2:47629753-47630583	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr2:47629880-47630763	GM12878	blood:	n/a	n/a
15	EP300	chr2:47629702-47630382	K562	blood:	n/a	chr2:47630033-47630043
16	YY1	chr2:47629834-47630858	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr2:47629852-47630558	GM12891	blood:	n/a	n/a
18	SP2	chr2:47629905-47630424	K562	blood:	n/a	n/a
19	POLR2A	chr2:47629697-47630799	GM19099	blood:	n/a	n/a
20	POLR2A	chr2:47629825-47630698	K562	blood:	n/a	n/a
21	FOXA1	chr2:47629729-47630323	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:47629869-47630369	MCF10A-Er-Src	breast:	n/a	n/a
23	NFIC	chr2:47629733-47630463	HepG2	liver:	n/a	n/a
24	YY1	chr2:47629894-47630115	GM12878	blood:	n/a	n/a
25	TAF1	chr2:47629904-47630443	Hela-S3	cervix:	n/a	n/a
26	MYC	chr2:47629537-47630874	K562	blood:	n/a	n/a
27	SP4	chr2:47629875-47630690	H1-hESC	embryonic stem cell:	n/a	chr2:47630645-47630661
28	CREB1	chr2:47629907-47630735	A549	lung:	n/a	n/a
29	PBX3	chr2:47629886-47630526	A549	lung:	n/a	n/a
30	CHD2	chr2:47629884-47630675	GM12878	blood:	n/a	n/a
31	PML	chr2:47629920-47630641	K562	blood:	n/a	n/a
32	MYBL2	chr2:47629660-47630848	HepG2	liver:	n/a	n/a
33	EP300	chr2:47629728-47630282	H1-hESC	embryonic stem cell:	n/a	chr2:47630033-47630043
34	CHD1	chr2:47629420-47629963	H1-hESC	embryonic stem cell:	n/a	n/a
35	E2F6	chr2:47629874-47630833	K562	blood:	n/a	chr2:47630264-47630271 chr2:47630261-47630272 chr2:47630599-47630606 chr2:47630129-47630141 chr2:47630159-47630168 chr2:47630264-47630271 chr2:47630599-47630606 chr2:47630263-47630271 chr2:47630263-47630272 chr2:47630746-47630756 chr2:47630260-47630272 chr2:47630264-47630271 chr2:47630599-47630606 chr2:47630598-47630610
36	POLR2A	chr2:47629859-47630914	Hela-S3	cervix:	n/a	n/a
37	EP300	chr2:47629689-47630557	A549	lung:	n/a	chr2:47630033-47630043
38	FOXP2	chr2:47629828-47630507	SK-N-MC	brain:	n/a	n/a
39	SP4	chr2:47629796-47630577	H1-hESC	embryonic stem cell:	n/a	n/a
40	POU2F2	chr2:47629825-47630387	GM12891	blood:	n/a	chr2:47630255-47630267
41	ZBTB7A	chr2:47629786-47630959	ECC-1	luminal epithelium:	n/a	chr2:47630216-47630227
42	REST	chr2:47629697-47630927	A549	lung:	n/a	n/a
43	GTF2F1	chr2:47629740-47630445	Hela-S3	cervix:	n/a	n/a
44	MAX	chr2:47629547-47630998	H1-hESC	embryonic stem cell:	n/a	n/a
45	ELK1	chr2:47629705-47630010	K562	blood:	n/a	n/a
46	POLR2A	chr2:47629810-47630759	GM12892	blood:	n/a	n/a
47	MBD4	chr2:47629591-47631719	HepG2	liver:	n/a	n/a
48	TCF12	chr2:47629726-47630833	ECC-1	luminal epithelium:	n/a	chr2:47630034-47630043 chr2:47630746-47630756
49	POLR2A	chr2:47629377-47631936	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAF1	chr2:47629898-47630516	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47402764..47405389-chr2:47627574..47630501,3	K562	blood:
2	chr2:47629900..47631449-chr2:48009384..48011204,2	K562	blood:
3	chr2:47592763..47599978-chr2:47628456..47631890,7	K562	blood:
4	chr2:47401987..47404848-chr2:47628320..47632624,5	MCF-7	breast:
5	chr2:47570416..47573787-chr2:47628581..47633320,5	MCF-7	breast:
6	chr2:47629202..47631353-chr20:52209184..52210821,2	MCF-7	breast:
7	chr2:47571726..47575826-chr2:47629274..47632481,3	MCF-7	breast:
8	chr2:47615615..47617911-chr2:47628205..47630073,2	MCF-7	breast:
9	chr2:47595241..47598489-chr2:47628033..47632018,10	MCF-7	breast:

Variant related genes	Relation type
MSH2	TF binding region
ENSG00000171940	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000234690	Chromatin interaction
ENSG00000143933	Chromatin interaction

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

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

rs_ID	r²[population]
rs57279207	1.00[AMR][1000 genomes]
rs57598249	1.00[AMR][1000 genomes]
rs58079492	1.00[AMR][1000 genomes]
rs59991093	1.00[AMR][1000 genomes]
rs61756466	1.00[AMR][1000 genomes]
rs72882780	1.00[AMR][1000 genomes]
rs72882797	1.00[AMR][1000 genomes]
rs72882798	1.00[AMR][1000 genomes]
rs72884619	1.00[AMR][1000 genomes]
rs72884688	1.00[AMR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	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	chr2:47629000-47630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:47629000-47631200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:47629000-47631200	Active TSS	Fetal Brain Female	brain
4	chr2:47629000-47631200	Active TSS	Fetal Intestine Large	intestine
5	chr2:47629200-47630000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:47629200-47630000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr2:47629200-47630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:47629200-47630000	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr2:47629200-47631000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47629200-47631000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:47629200-47631000	Active TSS	Fetal Lung	lung
12	chr2:47629200-47631000	Active TSS	Right Ventricle	heart
13	chr2:47629200-47631200	Active TSS	Fetal Kidney	kidney
14	chr2:47629200-47631600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:47629200-47632400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:47629400-47630000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:47629400-47630000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr2:47629400-47630000	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr2:47629400-47630000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr2:47629400-47630000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:47629400-47630000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr2:47629400-47630000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:47629400-47630000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr2:47629400-47630000	Flanking Active TSS	Liver	Liver
25	chr2:47629400-47630000	Flanking Active TSS	Fetal Thymus	thymus
26	chr2:47629400-47630000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:47629400-47630000	Flanking Active TSS	Dnd41	blood
28	chr2:47629400-47630000	Flanking Active TSS	Hela-S3	cervix
29	chr2:47629400-47630000	Flanking Active TSS	K562	blood
30	chr2:47629400-47630000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:47629400-47630000	Flanking Active TSS	NHEK	skin
32	chr2:47629400-47630000	Flanking Active TSS	Osteobl	bone
33	chr2:47629400-47630800	Active TSS	Brain Angular Gyrus	brain
34	chr2:47629400-47630800	Active TSS	Pancreas	Pancrea
35	chr2:47629400-47630800	Active TSS	Rectal Smooth Muscle	rectum
36	chr2:47629400-47631000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:47629400-47631000	Active TSS	Brain Anterior Caudate	brain
38	chr2:47629400-47631000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr2:47629400-47631200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:47629400-47631200	Active TSS	Colon Smooth Muscle	Colon
41	chr2:47629400-47631200	Active TSS	Psoas Muscle	Psoas
42	chr2:47629400-47631200	Active TSS	Stomach Mucosa	stomach
43	chr2:47629400-47631400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:47629400-47631400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr2:47629400-47632200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr2:47629600-47630000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:47629600-47630000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr2:47629600-47630000	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr2:47629600-47630000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:47629600-47630000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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