Variant report

Variant	rs539484721
Chromosome Location	chr21:45138519-45138520
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	chr21:45138501-45139510	PFSK-1	brain:	n/a	n/a
2	MXI1	chr21:45137887-45140344	SK-N-SH	brain:	n/a	n/a
3	ZBTB7A	chr21:45138308-45138933	ECC-1	luminal epithelium:	n/a	chr21:45138683-45138691
4	TEAD4	chr21:45138495-45139425	K562	blood:	n/a	n/a
5	TCF12	chr21:45138484-45139059	GM12878	blood:	n/a	n/a
6	ELF1	chr21:45138383-45139833	K562	blood:	n/a	chr21:45139436-45139445 chr21:45138528-45138540 chr21:45139607-45139616
7	CHD2	chr21:45138437-45140057	K562	blood:	n/a	chr21:45139547-45139557
8	MAX	chr21:45138430-45140132	ECC-1	luminal epithelium:	n/a	chr21:45138854-45138864
9	ELF1	chr21:45138149-45140445	GM12878	blood:	n/a	chr21:45140084-45140097 chr21:45139436-45139445 chr21:45138528-45138540 chr21:45139607-45139616
10	HEY1	chr21:45138343-45141309	K562	blood:	n/a	chr21:45140247-45140262 chr21:45138870-45138885
11	CHD2	chr21:45138510-45139554	Hela-S3	cervix:	n/a	n/a
12	EGR1	chr21:45138425-45139785	K562	blood:	n/a	chr21:45138677-45138687 chr21:45139428-45139441 chr21:45138915-45138925 chr21:45139431-45139440 chr21:45139430-45139440 chr21:45139429-45139440 chr21:45139428-45139441 chr21:45138611-45138624 chr21:45139428-45139442 chr21:45139424-45139446 chr21:45138910-45138923 chr21:45139378-45139387 chr21:45139427-45139442 chr21:45139430-45139440 chr21:45139431-45139441 chr21:45139428-45139441 chr21:45138911-45138925 chr21:45139428-45139441
13	E2F6	chr21:45138100-45139035	H1-hESC	embryonic stem cell:	n/a	chr21:45138915-45138924 chr21:45138427-45138436 chr21:45138589-45138596 chr21:45138919-45138929 chr21:45138588-45138600 chr21:45138589-45138596 chr21:45138589-45138596
14	E2F6	chr21:45138207-45139738	K562	blood:	n/a	chr21:45139556-45139568 chr21:45138915-45138924 chr21:45138427-45138436 chr21:45138589-45138596 chr21:45138919-45138929 chr21:45138588-45138600 chr21:45138589-45138596 chr21:45138589-45138596
15	HCFC1	chr21:45138157-45140065	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr21:45138481-45139427	H1-hESC	embryonic stem cell:	n/a	n/a
17	HDAC2	chr21:45138240-45140794	MCF-7	breast:	n/a	chr21:45138613-45138622 chr21:45139893-45139902
18	HDAC2	chr21:45138500-45139369	K562	blood:	n/a	chr21:45138613-45138622
19	POLR2A	chr21:45138197-45140874	K562	blood:	n/a	n/a
20	NR2F2	chr21:45138310-45140018	MCF-7	breast:	n/a	n/a
21	UBTF	chr21:45138517-45139814	K562	blood:	n/a	n/a
22	RAD21	chr21:45138508-45140259	IMR90	lung:	n/a	chr21:45139373-45139387 chr21:45139443-45139455 chr21:45139601-45139615 chr21:45139462-45139475 chr21:45140156-45140169 chr21:45139817-45139831
23	HMGN3	chr21:45138221-45140569	K562	blood:	n/a	n/a
24	EGR1	chr21:45138457-45140118	K562	blood:	n/a	chr21:45138677-45138687 chr21:45139428-45139441 chr21:45140040-45140051 chr21:45138915-45138925 chr21:45139431-45139440 chr21:45139430-45139440 chr21:45140085-45140094 chr21:45139429-45139440 chr21:45139428-45139441 chr21:45140040-45140051 chr21:45138611-45138624 chr21:45139428-45139442 chr21:45139424-45139446 chr21:45138910-45138923 chr21:45139378-45139387 chr21:45139427-45139442 chr21:45140040-45140054 chr21:45139430-45139440 chr21:45140042-45140051 chr21:45139431-45139441 chr21:45139428-45139441 chr21:45138911-45138925 chr21:45139428-45139441
25	NR2F2	chr21:45138499-45139290	K562	blood:	n/a	n/a
26	EBF1	chr21:45138383-45138669	GM12878	blood:	n/a	chr21:45138559-45138569 chr21:45138560-45138569 chr21:45138558-45138571
27	CREB1	chr21:45138518-45140427	HepG2	liver:	n/a	n/a
28	MAX	chr21:45138328-45140435	A549	lung:	n/a	chr21:45138854-45138864
29	TCF12	chr21:45138437-45140405	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr21:45138131-45141133	A549	lung:	n/a	n/a
31	POLR2A	chr21:45138465-45138662	A549	lung:	n/a	n/a
32	CTCF	chr21:45138460-45138610	GM06990	blood:	n/a	n/a
33	MAX	chr21:45138036-45140203	K562	blood:	n/a	chr21:45138854-45138864
34	EBF1	chr21:45138483-45138970	GM12878	blood:	n/a	chr21:45138559-45138569 chr21:45138560-45138569 chr21:45138558-45138571
35	BACH1	chr21:45138412-45140005	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF3	chr21:45138492-45139821	GM12878	blood:	n/a	chr21:45138864-45138877
37	POLR2A	chr21:45138349-45139561	PFSK-1	brain:	n/a	n/a
38	UBTF	chr21:45138444-45139851	K562	blood:	n/a	n/a
39	CTCF	chr21:45138469-45139147	K562	blood:	n/a	chr21:45138861-45138874
40	YY1	chr21:45138439-45139623	HepG2	liver:	n/a	chr21:45138912-45138926 chr21:45139239-45139259 chr21:45138463-45138474 chr21:45138915-45138924 chr21:45138864-45138878 chr21:45138875-45138889
41	TBP	chr21:45138477-45139382	K562	blood:	n/a	n/a
42	REST	chr21:45138276-45140085	H1-neurons	neurons:	n/a	chr21:45138483-45138493 chr21:45139733-45139746 chr21:45139368-45139381
43	RAD21	chr21:45138444-45139437	ECC-1	luminal epithelium:	n/a	chr21:45139373-45139387
44	PAX5	chr21:45138480-45139547	GM12892	blood:	n/a	chr21:45138873-45138882 chr21:45139378-45139387 chr21:45138871-45138880 chr21:45138614-45138623
45	MYC	chr21:45138343-45139517	K562	blood:	n/a	chr21:45138854-45138864
46	JUN	chr21:45137800-45139987	K562	blood:	n/a	n/a
47	MAX	chr21:45138043-45139461	H1-hESC	embryonic stem cell:	n/a	chr21:45138854-45138864
48	POLR2A	chr21:45138489-45139346	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr21:45138486-45139553	K562	blood:	n/a	n/a
50	POLR2A	chr21:45138495-45140314	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45103862..45106671-chr21:45138223..45140782,2	MCF-7	breast:
2	chr21:45136894..45141532-chr21:45205840..45211872,8	MCF-7	breast:
3	chr12:120727925..120730755-chr21:45138077..45140298,2	MCF-7	breast:
4	chr21:45138427..45140484-chr21:45209568..45212113,2	K562	blood:
5	chr21:45138069..45142004-chr21:45192681..45200004,8	MCF-7	breast:
6	chr21:45078168..45080813-chr21:45138258..45142239,4	K562	blood:
7	chr21:44393615..44395899-chr21:45138113..45140493,2	K562	blood:
8	chr21:45137445..45140588-chr21:45195005..45197401,3	K562	blood:
9	chr21:45137354..45140305-chr21:45163614..45165870,3	MCF-7	breast:
10	chr21:45105070..45107899-chr21:45137956..45140399,2	MCF-7	breast:
11	chr21:45137459..45139006-chr21:45757903..45760574,2	K562	blood:
12	chr17:62501067..62503702-chr21:45138284..45140156,2	MCF-7	breast:
13	chr21:44527246..44529052-chr21:45137735..45140365,2	K562	blood:
14	chr21:45138000..45143848-chr21:45206375..45212489,9	MCF-7	breast:
15	chr21:45077264..45080546-chr21:45137817..45144125,9	MCF-7	breast:
16	chr21:45137509..45139216-chr21:45209353..45211646,2	K562	blood:
17	chr21:45136545..45138543-chr21:45189331..45190847,2	K562	blood:
18	chr21:45137876..45142347-chr21:45194759..45200624,9	MCF-7	breast:
19	chr21:45136618..45138870-chr21:45233345..45236189,2	MCF-7	breast:
20	chr21:45136716..45139544-chr3:64006873..64009163,2	MCF-7	breast:

Variant related genes	Relation type
PDXK	TF binding region
ENSG00000232969	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000160213	Chromatin interaction
ENSG00000160226	Chromatin interaction
ENSG00000160209	Chromatin interaction
ENSG00000160208	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000160207	Chromatin interaction
ENSG00000160199	Chromatin interaction
ENSG00000160214	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000258890	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1066613	chr21:45108233-45148136	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv3424986	chr21:45118675-45158421	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv3329872	chr21:45118725-45158757	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv913875	chr21:45119629-45191005	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription 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	31 gene(s)	inside rSNPs	diseases
9	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv587701	chr21:45128190-45181446	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv459290	chr21:45128454-45191139	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv587702	chr21:45128454-45191139	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv913877	chr21:45133868-45163689	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
14	nsv913878	chr21:45133868-45170285	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	esv3387851	chr21:45137749-45140297	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
17	esv3406453	chr21:45138149-45140697	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45138000-45138600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:45138000-45138600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr21:45138000-45138600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr21:45138000-45138600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr21:45138000-45138600	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr21:45138000-45138600	Enhancers	Spleen	Spleen
7	chr21:45138000-45138600	Flanking Active TSS	GM12878-XiMat	blood
8	chr21:45138000-45138600	Flanking Active TSS	K562	blood
9	chr21:45138000-45138800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr21:45138000-45139000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr21:45138000-45139200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr21:45138000-45139800	Active TSS	Brain Hippocampus Middle	brain
13	chr21:45138000-45140000	Active TSS	Rectal Smooth Muscle	rectum
14	chr21:45138000-45140000	Active TSS	Osteobl	bone
15	chr21:45138000-45140400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr21:45138200-45138600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr21:45138200-45138600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:45138200-45138600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr21:45138200-45138600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr21:45138200-45138600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr21:45138200-45138600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:45138200-45138600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr21:45138200-45138600	Flanking Active TSS	Colonic Mucosa	Colon
24	chr21:45138200-45138600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr21:45138200-45138600	Enhancers	Fetal Lung	lung
26	chr21:45138200-45138600	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr21:45138200-45138600	Flanking Active TSS	Placenta	Placenta
28	chr21:45138200-45138600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr21:45138200-45138600	Enhancers	Small Intestine	intestine
30	chr21:45138200-45138600	Flanking Active TSS	Hela-S3	cervix
31	chr21:45138200-45138600	Flanking Active TSS	NHLF	lung
32	chr21:45138200-45138800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr21:45138200-45138800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr21:45138200-45138800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr21:45138200-45138800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr21:45138200-45138800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr21:45138200-45138800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr21:45138200-45138800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr21:45138200-45138800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:45138200-45138800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr21:45138200-45138800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr21:45138200-45138800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr21:45138200-45138800	Flanking Active TSS	HMEC	breast
44	chr21:45138200-45139800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr21:45138200-45139800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr21:45138200-45139800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr21:45138200-45139800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr21:45138200-45139800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr21:45138200-45139800	Active TSS	Fetal Brain Female	brain
50	chr21:45138200-45139800	Active TSS	NH-A	brain

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