Variant report

Variant	rs2288323
Chromosome Location	chr2:179343912-179343913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:435)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:435 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179342918-179344002	K562	blood:	n/a	n/a
2	POLR2A	chr2:179342855-179344105	GM12892	blood:	n/a	n/a
3	ZNF217	chr2:179343869-179344067	MCF-7	breast:	n/a	n/a
4	CTCF	chr2:179343820-179343970	AG04449	skin:	n/a	n/a
5	CTCF	chr2:179343799-179344046	Medullo	brain:	n/a	n/a
6	POLR2A	chr2:179342862-179344194	HL-60	blood:	n/a	n/a
7	RCOR1	chr2:179342458-179344495	K562	blood:	n/a	n/a
8	POLR2A	chr2:179343633-179344105	HL-60	blood:	n/a	n/a
9	POLR2A	chr2:179342874-179344152	GM12892	blood:	n/a	n/a
10	YY1	chr2:179342933-179344094	GM12878	blood:	n/a	chr2:179343379-179343388
11	POLR2A	chr2:179342878-179344068	U87	brain:	n/a	n/a
12	POLR2A	chr2:179343019-179344012	Gliobla	brain:	n/a	n/a
13	EP300	chr2:179343703-179344009	GM12878	blood:	n/a	chr2:179343929-179343945
14	RAD21	chr2:179343759-179344125	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:179343098-179343957	Hela-S3	cervix:	n/a	n/a
16	CHD2	chr2:179342907-179344082	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:179342670-179344007	GM18505	blood:	n/a	n/a
18	RCOR1	chr2:179342619-179344501	K562	blood:	n/a	n/a
19	CTCF	chr2:179343803-179344066	LNCaP	prostate:	n/a	n/a
20	CTCF	chr2:179343840-179343990	GM12874	blood:	n/a	n/a
21	MYC	chr2:179342870-179344060	NB4	blood:	n/a	chr2:179343356-179343366
22	TEAD4	chr2:179342936-179344246	K562	blood:	n/a	n/a
23	POLR2A	chr2:179343674-179343984	GM12878	blood:	n/a	n/a
24	CTCF	chr2:179343860-179344010	HL-60	blood:	n/a	n/a
25	BCL3	chr2:179343686-179344655	A549	lung:	n/a	chr2:179344526-179344535
26	CTCF	chr2:179343830-179344000	SK-N-SH_RA	brain:	n/a	n/a
27	BCLAF1	chr2:179343066-179344152	GM12878	blood:	n/a	chr2:179343385-179343398 chr2:179343392-179343405
28	RAD21	chr2:179343769-179344115	K562	blood:	n/a	n/a
29	SETDB1	chr2:179343632-179344613	U2OS	brain:	n/a	n/a
30	CTCF	chr2:179343789-179344083	K562	blood:	n/a	n/a
31	CTCF	chr2:179343880-179344030	NB4	blood:	n/a	n/a
32	CREB1	chr2:179343610-179344110	A549	lung:	n/a	n/a
33	RUNX3	chr2:179343106-179344093	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:179342973-179344041	PFSK-1	brain:	n/a	n/a
35	BCLAF1	chr2:179343109-179344149	GM12878	blood:	n/a	chr2:179343385-179343398 chr2:179343392-179343405
36	CREB1	chr2:179342886-179344202	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:179342908-179344020	HepG2	liver:	n/a	n/a
38	REST	chr2:179342457-179344429	H1-neurons	neurons:	n/a	chr2:179343393-179343406 chr2:179343393-179343406
39	SMC3	chr2:179343126-179344380	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr2:179343640-179344121	MCF-7	breast:	n/a	n/a
41	CTCF	chr2:179343840-179343990	HRE	kidney:	n/a	n/a
42	TCF7L2	chr2:179342941-179344053	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr2:179343860-179344010	GM12878	blood:	n/a	n/a
44	TAF1	chr2:179343727-179343989	K562	blood:	n/a	n/a
45	CUX1	chr2:179343507-179344014	GM12878	blood:	n/a	n/a
46	HDAC2	chr2:179343633-179344106	MCF-7	breast:	n/a	chr2:179343916-179343930
47	RELA	chr2:179342938-179344137	GM18505	blood:	n/a	n/a
48	CTCF	chr2:179343840-179343990	HPAF	blood vessel:	n/a	n/a
49	CTCF	chr2:179343833-179344057	HUVEC	blood vessel:	n/a	n/a
50	HDAC2	chr2:179343633-179344162	MCF-7	breast:	n/a	chr2:179343916-179343930

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:179343871-179343921	GM12891	blood:	n/a
2	chr2:179343871-179343921	MCF10A-Er-Src	breast:	n/a
3	chr2:179343871-179343921	HPAEpiC	pulmonary alveolar:	n/a
4	chr2:179343871-179343921	AG04449	skin:	fetal
5	chr2:179343871-179343921	NHDF-neo	bronchial:	n/a
6	chr2:179343871-179343921	AG09309	skin:	n/a
7	chr2:179343871-179343921	GM12878	blood:	n/a
8	chr2:179343871-179343921	ECC-1	luminal epithelium:	n/a
9	chr2:179343871-179343921	HRE	kidney:	n/a
10	chr2:179343871-179343921	HUVEC	blood vessel:	n/a
11	chr2:179343871-179343921	PFSK-1	brain:	n/a
12	chr2:179343871-179343921	PrEC	prostate:	n/a
13	chr2:179343871-179343921	AG10803	skin:	n/a
14	chr2:179343871-179343921	RPTEC	kidney:	n/a
15	chr2:179343871-179343921	ovcar-3	ovarian:	n/a
16	chr2:179343871-179343921	SKMC	muscle:	n/a
17	chr2:179343871-179343921	PANC-1	pancreas:	n/a
18	chr2:179343871-179343921	CMK	blood:	n/a
19	chr2:179343871-179343921	HCT-116	colon:	n/a
20	chr2:179343871-179343921	HCM	heart:	n/a
21	chr2:179343871-179343921	HMEC	breast:	n/a
22	chr2:179343871-179343921	LNCaP	prostate:	n/a
23	chr2:179343871-179343921	NT2-D1	testis:	n/a
24	chr2:179343871-179343921	AG04450	lung:	fetal
25	chr2:179343871-179343921	NHBE	bronchial:	n/a
26	chr2:179343871-179343921	ProgFib	skin:	n/a
27	chr2:179343871-179343921	BJ	skin:	n/a
28	chr2:179343871-179343921	Jurkat	blood:	n/a
29	chr2:179343871-179343921	NH-A	brain:	n/a
30	chr2:179343871-179343921	H1-hESC	embryonic stem cell:	embryo
31	chr2:179343871-179343921	T-47D	breast:	n/a
32	chr2:179343871-179343921	SK-N-SH	brain:	n/a
33	chr2:179343871-179343921	HEK293	kidney:	embryo
34	chr2:179343871-179343921	Hepatocyte	liver:	n/a
35	chr2:179343871-179343921	HCF	heart:	n/a
36	chr2:179343871-179343921	GM06990	blood:	n/a
37	chr2:179343871-179343921	BE2_C	brain:	n/a
38	chr2:179343871-179343921	IMR90	lung:	fetal
39	chr2:179343871-179343921	HRPEpiC	eye:	n/a
40	chr2:179343871-179343921	HAEpiC	amniotic membrane:	n/a
41	chr2:179343871-179343921	U87	brain:	n/a
42	chr2:179343871-179343921	A549	lung:	n/a
43	chr2:179343871-179343921	MCF-7	breast:	n/a
44	chr2:179343871-179343921	Caco-2	colon:	n/a
45	chr2:179343871-179343921	GM12892	blood:	n/a
46	chr2:179343871-179343921	K562	blood:	n/a
47	chr2:179343871-179343921	SAEC	small airway:	n/a
48	chr2:179343871-179343921	SK-N-MC	brain:	n/a
49	chr2:179343871-179343921	HL-60	blood:	n/a
50	chr2:179343871-179343921	Hela-S3	cervix:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:76970332..76972740-chr2:179341961..179344883,2	MCF-7	breast:
2	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
3	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
4	chr2:178976808..178978488-chr2:179342162..179344754,2	MCF-7	breast:
5	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
6	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
7	chr2:179343391..179346043-chr2:179387218..179389955,4	K562	blood:
8	chr2:179314444..179318442-chr2:179340876..179346721,19	MCF-7	breast:
9	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
10	chr2:178127221..178129853-chr2:179341742..179345099,3	K562	blood:
11	chr2:179308416..179311292-chr2:179342166..179344945,2	MCF-7	breast:
12	chr2:179278151..179280958-chr2:179342121..179344961,4	K562	blood:

No data

Variant related genes	Relation type
PLEKHA3	TF binding region
FKBP7	TF binding region
PLEKHA3	CpG island
FKBP7	CpG island
ENSG00000237298	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000165637	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11687811	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2278196	0.81[CHD][hapmap]
rs62176091	0.81[EUR][1000 genomes]
rs62176101	0.88[EUR][1000 genomes]
rs62176104	0.88[EUR][1000 genomes]
rs62176114	0.87[EUR][1000 genomes]
rs62176142	0.96[ASN][1000 genomes]
rs9967820	0.88[ASW][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 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	chr2:179341200-179346000	Active TSS	Fetal Brain Female	brain
2	chr2:179341400-179344200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:179341600-179344200	Active TSS	Fetal Lung	lung
4	chr2:179341800-179344000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:179341800-179344000	Active TSS	Ovary	ovary
6	chr2:179341800-179345000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:179341800-179345600	Active TSS	Brain Germinal Matrix	brain
8	chr2:179341800-179345800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:179342000-179344000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:179342000-179344000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:179342000-179346200	Active TSS	Fetal Kidney	kidney
12	chr2:179342000-179346400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:179342000-179346400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:179342000-179346600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:179342200-179344000	Active TSS	K562	blood
16	chr2:179342200-179344400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:179342200-179345800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:179342200-179347200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:179342400-179344000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:179342400-179344000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:179342400-179344000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr2:179342400-179344000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:179342400-179344000	Active TSS	Osteobl	bone
24	chr2:179342400-179344200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:179342400-179344200	Active TSS	Fetal Intestine Small	intestine
26	chr2:179342400-179344200	Active TSS	A549	lung
27	chr2:179342400-179344200	Active TSS	Hela-S3	cervix
28	chr2:179342400-179344200	Active TSS	NHDF-Ad	bronchial
29	chr2:179342400-179344400	Active TSS	Fetal Stomach	stomach
30	chr2:179342400-179344600	Active TSS	Fetal Muscle Trunk	muscle
31	chr2:179342400-179344800	Active TSS	Fetal Brain Male	brain
32	chr2:179342400-179346200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr2:179342400-179346200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr2:179342400-179346200	Active TSS	Psoas Muscle	Psoas
35	chr2:179342400-179346200	Active TSS	HSMM	muscle
36	chr2:179342400-179346600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:179342400-179347000	Active TSS	HSMMtube	muscle
38	chr2:179342600-179344000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:179342600-179344000	Active TSS	Colon Smooth Muscle	Colon
40	chr2:179342600-179344000	Bivalent/Poised TSS	HepG2	liver
41	chr2:179342600-179344200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr2:179342600-179344200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr2:179342600-179344200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:179342600-179344200	Active TSS	Brain Substantia Nigra	brain
45	chr2:179342600-179344400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:179342600-179345000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:179342600-179345800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr2:179342600-179345800	Active TSS	Thymus	Thymus
49	chr2:179342600-179346000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr2:179342600-179346200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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