Variant report

Variant	rs2287341
Chromosome Location	chr2:53995380-53995381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:263)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:263 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr2:53994532-53995418	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr2:53994390-53995707	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr2:53994434-53995561	GM12878	blood:	n/a	n/a
4	GATA2	chr2:53994546-53995474	SH-SY5Y	brain:	n/a	chr2:53994842-53994849
5	POLR2A	chr2:53994442-53995493	GM12878	blood:	n/a	n/a
6	HCFC1	chr2:53993642-53995965	Hela-S3	cervix:	n/a	n/a
7	RELA	chr2:53994495-53995564	GM19193	blood:	n/a	n/a
8	RELA	chr2:53994431-53995647	GM12891	blood:	n/a	n/a
9	POLR2A	chr2:53994840-53995450	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr2:53994509-53995639	SK-N-SH	brain:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
11	NR2F2	chr2:53994512-53995387	K562	blood:	n/a	n/a
12	POLR2A	chr2:53994421-53995632	NB4	blood:	n/a	n/a
13	NFATC1	chr2:53994351-53995784	GM12878	blood:	n/a	chr2:53994386-53994399
14	POLR2A	chr2:53994421-53995461	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:53994421-53995690	Raji	blood:	n/a	n/a
16	CTBP2	chr2:53994706-53995554	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD2	chr2:53994486-53995638	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr2:53994807-53995527	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr2:53994390-53995785	A549	lung:	n/a	n/a
20	TBL1XR1	chr2:53994525-53995396	K562	blood:	n/a	n/a
21	SIN3A	chr2:53994428-53995720	H1-hESC	embryonic stem cell:	n/a	chr2:53995165-53995178
22	MYC	chr2:53994263-53995599	K562	blood:	n/a	n/a
23	TAF1	chr2:53994466-53995528	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:53995224-53995442	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:53994388-53995728	GM12878	blood:	n/a	n/a
26	ZEB1	chr2:53994834-53995522	GM12878	blood:	n/a	n/a
27	TAF1	chr2:53994373-53995493	A549	lung:	n/a	n/a
28	HDAC2	chr2:53994456-53995562	MCF-7	breast:	n/a	chr2:53994827-53994841
29	RELA	chr2:53994564-53995643	GM18951	blood:	n/a	n/a
30	YY1	chr2:53994545-53995599	GM12892	blood:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
31	MAX	chr2:53994496-53995470	K562	blood:	n/a	n/a
32	POLR2A	chr2:53994423-53995711	GM12891	blood:	n/a	n/a
33	PBX3	chr2:53994567-53995484	A549	lung:	n/a	n/a
34	BHLHE40	chr2:53994441-53995656	K562	blood:	n/a	n/a
35	MYC	chr2:53994889-53995470	MCF-7	breast:	n/a	n/a
36	BHLHE40	chr2:53995009-53995597	GM12878	blood:	n/a	n/a
37	MAX	chr2:53994746-53995621	SK-N-SH	brain:	n/a	n/a
38	BCLAF1	chr2:53994376-53995479	GM12878	blood:	n/a	chr2:53994965-53994978
39	MXI1	chr2:53994521-53995634	Hela-S3	cervix:	n/a	n/a
40	MBD4	chr2:53994375-53995459	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:53994792-53995432	MCF-7	breast:	n/a	n/a
42	RELA	chr2:53994483-53995560	GM19099	blood:	n/a	n/a
43	POLR2A	chr2:53994323-53995521	K562	blood:	n/a	n/a
44	YY1	chr2:53994457-53995611	GM12878	blood:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
45	CHD2	chr2:53994516-53995475	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:53994411-53995668	HepG2	liver:	n/a	n/a
47	BCL3	chr2:53994333-53995803	A549	lung:	n/a	chr2:53994965-53994978
48	MAX	chr2:53994729-53995590	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr2:53994424-53996024	PFSK-1	brain:	n/a	n/a
50	TEAD4	chr2:53994263-53995387	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:53995338-53995388	LNCaP	prostate:	n/a
2	chr2:53995338-53995388	SK-N-SH	brain:	n/a
3	chr2:53995338-53995388	HUVEC	blood vessel:	n/a
4	chr2:53995338-53995388	GM06990	blood:	n/a
5	chr2:53995338-53995388	ovcar-3	ovarian:	n/a
6	chr2:53995338-53995388	HRPEpiC	eye:	n/a
7	chr2:53995338-53995388	CMK	blood:	n/a
8	chr2:53995338-53995388	AG04450	lung:	fetal
9	chr2:53995338-53995388	NB4	blood:	n/a
10	chr2:53995338-53995388	PFSK-1	brain:	n/a
11	chr2:53995338-53995388	HEK293	kidney:	embryo
12	chr2:53995338-53995388	PANC-1	pancreas:	n/a
13	chr2:53995338-53995388	T-47D	breast:	n/a
14	chr2:53995338-53995388	HL-60	blood:	n/a
15	chr2:53995338-53995388	HAEpiC	amniotic membrane:	n/a
16	chr2:53995338-53995388	MCF10A-Er-Src	breast:	n/a
17	chr2:53995338-53995388	SKMC	muscle:	n/a
18	chr2:53995338-53995388	HEEpiC	esophagus:	n/a
19	chr2:53995338-53995388	GM12891	blood:	n/a
20	chr2:53995338-53995388	GM12892	blood:	n/a
21	chr2:53995338-53995388	Jurkat	blood:	n/a
22	chr2:53995338-53995388	HNPCEpiC	eye:	n/a
23	chr2:53995338-53995388	AG10803	skin:	n/a
24	chr2:53995338-53995388	AG04449	skin:	fetal
25	chr2:53995338-53995388	NH-A	brain:	n/a
26	chr2:53995338-53995388	HRE	kidney:	n/a
27	chr2:53995338-53995388	AG09309	skin:	n/a
28	chr2:53995338-53995388	Hela-S3	cervix:	n/a
29	chr2:53995338-53995388	PrEC	prostate:	n/a
30	chr2:53995338-53995388	SK-N-SH_RA	brain:	n/a
31	chr2:53995338-53995388	BE2_C	brain:	n/a
32	chr2:53995338-53995388	NHBE	bronchial:	n/a
33	chr2:53995338-53995388	IMR90	lung:	fetal
34	chr2:53995338-53995388	U87	brain:	n/a
35	chr2:53995338-53995388	HepG2	liver:	n/a
36	chr2:53995338-53995388	ProgFib	skin:	n/a
37	chr2:53995338-53995388	MCF-7	breast:	n/a
38	chr2:53995338-53995388	A549	lung:	n/a
39	chr2:53995338-53995388	RPTEC	kidney:	n/a
40	chr2:53995338-53995388	SK-N-MC	brain:	n/a
41	chr2:53995338-53995388	Hepatocyte	liver:	n/a
42	chr2:53995338-53995388	HCPEpiC	choroid plexus:	n/a
43	chr2:53995338-53995388	K562	blood:	n/a
44	chr2:53995338-53995388	HPAEpiC	pulmonary alveolar:	n/a
45	chr2:53995338-53995388	H1-hESC	embryonic stem cell:	embryo
46	chr2:53995338-53995388	BJ	skin:	n/a
47	chr2:53995338-53995388	AoSMC	blood vessel:	n/a
48	chr2:53995338-53995388	HRCEpiC	kidney:	n/a
49	chr2:53995338-53995388	ECC-1	luminal epithelium:	n/a
50	chr2:53995338-53995388	NT2-D1	testis:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
2	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
3	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

No data

Variant related genes	Relation type
GPR75-ASB3	TF binding region
GPR75-ASB3	CpG island
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10188007	0.84[ASN][1000 genomes]
rs10192154	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12613353	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12617599	0.83[ASN][1000 genomes]
rs13397311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2080721	0.85[ASN][1000 genomes]
rs2177793	0.84[ASN][1000 genomes]
rs2287348	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2357697	0.84[ASN][1000 genomes]
rs3770393	0.94[ASN][1000 genomes]
rs56939249	0.83[ASN][1000 genomes]
rs6545366	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545370	0.84[ASN][1000 genomes]
rs6737681	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597034	0.84[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr2:53994000-53995800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:53994000-53996200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:53994200-53995400	Active TSS	Fetal Muscle Trunk	muscle
4	chr2:53994200-53995400	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr2:53994200-53995600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:53994200-53995600	Active TSS	Rectal Smooth Muscle	rectum
7	chr2:53994200-53995600	Active TSS	HSMMtube	muscle
8	chr2:53994200-53995600	Active TSS	NHLF	lung
9	chr2:53994200-53995800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:53994200-53995800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:53994200-53995800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:53994200-53995800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:53994200-53995800	Active TSS	Psoas Muscle	Psoas
14	chr2:53994200-53995800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr2:53994200-53995800	Active TSS	HMEC	breast
16	chr2:53994200-53996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:53994200-53996000	Active TSS	GM12878-XiMat	blood
18	chr2:53994200-53996000	Active TSS	K562	blood
19	chr2:53994200-53996200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:53994200-53996400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:53994200-53996400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:53994400-53995400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:53994400-53995400	Active TSS	Primary B cells from peripheral blood	blood
25	chr2:53994400-53995400	Active TSS	Primary T cells from cord blood	blood
26	chr2:53994400-53995400	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:53994400-53995400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr2:53994400-53995400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:53994400-53995400	Active TSS	Brain Hippocampus Middle	brain
30	chr2:53994400-53995400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:53994400-53995400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:53994400-53995400	Active TSS	Brain Substantia Nigra	brain
33	chr2:53994400-53995400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:53994400-53995400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:53994400-53995400	Active TSS	Fetal Brain Male	brain
36	chr2:53994400-53995400	Active TSS	Fetal Heart	heart
37	chr2:53994400-53995400	Active TSS	Fetal Lung	lung
38	chr2:53994400-53995400	Active TSS	Lung	lung
39	chr2:53994400-53995400	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr2:53994400-53995400	Bivalent/Poised TSS	HepG2	liver
41	chr2:53994400-53995600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:53994400-53995600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:53994400-53995600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr2:53994400-53995600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr2:53994400-53995600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:53994400-53995600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:53994400-53995600	Active TSS	Aorta	Aorta
48	chr2:53994400-53995600	Active TSS	Brain Angular Gyrus	brain
49	chr2:53994400-53995600	Active TSS	Colonic Mucosa	Colon
50	chr2:53994400-53995600	Active TSS	Colon Smooth Muscle	Colon

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