Variant report

Variant	rs1863333
Chromosome Location	chr2:47629604-47629605
allele	A/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	RUNX3	chr2:47629200-47630855	GM12878	blood:	n/a	n/a
2	MYC	chr2:47629537-47630874	K562	blood:	n/a	n/a
3	CHD1	chr2:47629420-47629963	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr2:47629547-47630998	H1-hESC	embryonic stem cell:	n/a	n/a
5	MBD4	chr2:47629591-47631719	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:47629377-47631936	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr2:47629312-47631278	A549	lung:	n/a	chr2:47630034-47630043 chr2:47630746-47630756
8	NRF1	chr2:47629464-47631365	SK-N-SH	brain:	n/a	chr2:47630099-47630113 chr2:47630124-47630135
9	FOS	chr2:47629562-47630207	HUVEC	blood vessel:	n/a	chr2:47629716-47629727
10	HDAC2	chr2:47629526-47630614	H1-hESC	embryonic stem cell:	n/a	chr2:47630034-47630043
11	PML	chr2:47629281-47631042	GM12878	blood:	n/a	n/a
12	SP1	chr2:47629592-47630442	H1-hESC	embryonic stem cell:	n/a	chr2:47630148-47630169 chr2:47629871-47629885 chr2:47630279-47630289
13	TEAD4	chr2:47629487-47630793	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:47629566-47630621	PANC-1	pancreas:	n/a	n/a
15	RCOR1	chr2:47629437-47630802	K562	blood:	n/a	n/a
16	NFIC	chr2:47629491-47630718	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:47629504-47630905	SK-N-SH	brain:	n/a	n/a
18	MAX	chr2:47629581-47630916	HCT-116	colon:	n/a	n/a
19	MAX	chr2:47629537-47631228	Hela-S3	cervix:	n/a	n/a
20	E2F6	chr2:47629470-47631130	A549	lung:	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
21	RCOR1	chr2:47629600-47631266	Hela-S3	cervix:	n/a	n/a
22	STAT5A	chr2:47629564-47631180	GM12878	blood:	n/a	n/a
23	REST	chr2:47629510-47631387	H1-neurons	neurons:	n/a	n/a
24	MAX	chr2:47629505-47631391	A549	lung:	n/a	n/a
25	POLR2A	chr2:47629535-47630873	GM12891	blood:	n/a	n/a
26	POLR2A	chr2:47629433-47631234	Hela-S3	cervix:	n/a	n/a
27	MAX	chr2:47629600-47631082	ECC-1	luminal epithelium:	n/a	n/a
28	MYBL2	chr2:47629529-47631119	HepG2	liver:	n/a	n/a
29	POLR2A	chr2:47629470-47630595	HUVEC	blood vessel:	n/a	n/a
30	TEAD4	chr2:47629502-47631005	K562	blood:	n/a	n/a
31	MXI1	chr2:47629461-47631111	IMR90	lung:	n/a	n/a
32	IRF1	chr2:47629560-47631741	K562	blood:	n/a	chr2:47630159-47630168
33	MAX	chr2:47629582-47631391	A549	lung:	n/a	n/a
34	RFX5	chr2:47629526-47631116	Hela-S3	cervix:	n/a	n/a
35	HCFC1	chr2:47629440-47631686	Hela-S3	cervix:	n/a	n/a
36	RCOR1	chr2:47629519-47631850	K562	blood:	n/a	n/a
37	NR2F2	chr2:47629539-47632019	K562	blood:	n/a	n/a
38	POLR2A	chr2:47629407-47630879	GM12878	blood:	n/a	n/a
39	FOSL2	chr2:47629506-47630806	A549	lung:	n/a	chr2:47630259-47630268
40	MTA3	chr2:47628991-47631268	GM12878	blood:	n/a	n/a
41	MXI1	chr2:47629064-47631866	SK-N-SH	brain:	n/a	n/a
42	ATF2	chr2:47629550-47630278	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3AK20	chr2:47629475-47631452	MCF-7	breast:	n/a	n/a
44	CBX3	chr2:47629583-47630936	K562	blood:	n/a	n/a
45	FOXA2	chr2:47629477-47630537	HepG2	liver:	n/a	n/a
46	E2F6	chr2:47629544-47630963	H1-hESC	embryonic stem cell:	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
47	TAF1	chr2:47629551-47630638	A549	lung:	n/a	n/a
48	BACH1	chr2:47629597-47631077	H1-hESC	embryonic stem cell:	n/a	n/a
49	JUND	chr2:47629560-47630837	K562	blood:	n/a	chr2:47629716-47629727 chr2:47630259-47630268

No.	Distal block	Cell Line	Cell type
1	chr2:47402764..47405389-chr2:47627574..47630501,3	K562	blood:
2	chr2:47592763..47599978-chr2:47628456..47631890,7	K562	blood:
3	chr2:47402764..47405044-chr2:47627574..47629731,2	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	chr2:47607664..47610611-chr2:47628092..47629761,2	K562	blood:
7	chr2:47629202..47631353-chr20:52209184..52210821,2	MCF-7	breast:
8	chr2:47571726..47575826-chr2:47629274..47632481,3	MCF-7	breast:
9	chr2:47615615..47617911-chr2:47628205..47630073,2	MCF-7	breast:
10	chr2:47595241..47598489-chr2:47628033..47632018,10	MCF-7	breast:

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

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10173799	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10179950	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1126497	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11686285	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999725	0.91[AMR][1000 genomes]
rs2162122	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923559	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4073491	0.80[AMR][1000 genomes]
rs4952885	0.88[AMR][1000 genomes]
rs62139705	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544987	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757310	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71399026	0.82[AMR][1000 genomes]
rs7587478	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7587654	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47628800-47629800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:47629000-47629800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:47629000-47629800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:47629000-47629800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:47629000-47629800	Flanking Active TSS	GM12878-XiMat	blood
6	chr2:47629000-47630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:47629000-47631200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:47629000-47631200	Active TSS	Fetal Brain Female	brain
9	chr2:47629000-47631200	Active TSS	Fetal Intestine Large	intestine
10	chr2:47629200-47629800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:47629200-47629800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:47629200-47629800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:47629200-47629800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr2:47629200-47630000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:47629200-47630000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr2:47629200-47630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:47629200-47630000	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr2:47629200-47631000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:47629200-47631000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:47629200-47631000	Active TSS	Fetal Lung	lung
21	chr2:47629200-47631000	Active TSS	Right Ventricle	heart
22	chr2:47629200-47631200	Active TSS	Fetal Kidney	kidney
23	chr2:47629200-47631600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:47629200-47632400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr2:47629400-47629800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:47629400-47629800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr2:47629400-47629800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:47629400-47629800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:47629400-47629800	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr2:47629400-47629800	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr2:47629400-47629800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:47629400-47629800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr2:47629400-47629800	Flanking Active TSS	Colonic Mucosa	Colon
34	chr2:47629400-47629800	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr2:47629400-47629800	Flanking Active TSS	Fetal Stomach	stomach
36	chr2:47629400-47629800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr2:47629400-47629800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr2:47629400-47629800	Flanking Active TSS	Thymus	Thymus
39	chr2:47629400-47629800	Flanking Active TSS	A549	lung
40	chr2:47629400-47629800	Flanking Active TSS	HepG2	liver
41	chr2:47629400-47630000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:47629400-47630000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr2:47629400-47630000	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr2:47629400-47630000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr2:47629400-47630000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:47629400-47630000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:47629400-47630000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:47629400-47630000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr2:47629400-47630000	Flanking Active TSS	Liver	Liver
50	chr2:47629400-47630000	Flanking Active TSS	Fetal Thymus	thymus

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