Variant report

Variant	rs9653241
Chromosome Location	chr2:182322792-182322793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:111)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:111 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr2:182321777-182323143	H1-hESC	embryonic stem cell:	n/a	chr2:182322628-182322639 chr2:182322628-182322639 chr2:182322745-182322755
2	POLR2A	chr2:182321261-182323289	GM12878	blood:	n/a	n/a
3	MAX	chr2:182321322-182323296	GM12878	blood:	n/a	chr2:182321353-182321362
4	NRF1	chr2:182321388-182322798	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:182321194-182324105	GM12878	blood:	n/a	n/a
6	TAF1	chr2:182322720-182323021	GM12892	blood:	n/a	n/a
7	PML	chr2:182322511-182322923	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr2:182322434-182322834	SK-N-SH	brain:	n/a	n/a
9	RELA	chr2:182321275-182323185	GM18951	blood:	n/a	n/a
10	POLR2A	chr2:182321218-182323235	GM18526	blood:	n/a	n/a
11	POLR2A	chr2:182321259-182324033	GM15510	blood:	n/a	n/a
12	USF1	chr2:182322764-182323000	GM12878	blood:	n/a	n/a
13	MAX	chr2:182322296-182323081	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr2:182322785-182322974	GM19239	blood:	n/a	n/a
15	CHD2	chr2:182322613-182323035	GM12878	blood:	n/a	n/a
16	EBF1	chr2:182322507-182323122	GM12878	blood:	n/a	n/a
17	BCLAF1	chr2:182321245-182323100	GM12878	blood:	n/a	chr2:182321908-182321917 chr2:182321780-182321793
18	RAD21	chr2:182321380-182322802	SK-N-SH_RA	brain:	n/a	chr2:182321712-182321719
19	MAX	chr2:182321760-182323167	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF263	chr2:182321348-182323054	HEK293-T-REx	kidney:	n/a	chr2:182321560-182321569 chr2:182322812-182322821
21	TBL1XR1	chr2:182322754-182323438	GM12878	blood:	n/a	n/a
22	CTBP2	chr2:182321248-182323159	H1-hESC	embryonic stem cell:	n/a	n/a
23	STAT5A	chr2:182322381-182323037	GM12878	blood:	n/a	chr2:182322664-182322672
24	POLR2A	chr2:182321262-182323185	GM12891	blood:	n/a	n/a
25	FOXM1	chr2:182321252-182322951	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:182321155-182323202	GM18951	blood:	n/a	n/a
27	EBF1	chr2:182322651-182323074	GM12878	blood:	n/a	n/a
28	ZNF143	chr2:182322697-182323045	H1-hESC	embryonic stem cell:	n/a	chr2:182322800-182322818
29	MAX	chr2:182321792-182323059	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr2:182321149-182322969	SK-N-SH	brain:	n/a	chr2:182321712-182321719
31	POLR2A	chr2:182321408-182323301	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:182322741-182322917	MCF-7	breast:	n/a	n/a
33	E2F6	chr2:182321280-182323114	H1-hESC	embryonic stem cell:	n/a	chr2:182322628-182322639 chr2:182322628-182322639 chr2:182322745-182322755
34	SPI1	chr2:182321204-182322910	HL-60	blood:	n/a	chr2:182321903-182321916 chr2:182321549-182321556 chr2:182321562-182321575
35	ATF2	chr2:182321209-182323049	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:182322567-182323135	PFSK-1	brain:	n/a	n/a
37	EGR1	chr2:182322661-182322993	GM12878	blood:	n/a	chr2:182322807-182322821 chr2:182322800-182322813
38	CTCF	chr2:182321058-182322900	SK-N-SH	brain:	n/a	n/a
39	MAX	chr2:182321706-182323060	SK-N-SH	brain:	n/a	n/a
40	PAX5	chr2:182322621-182322955	GM12892	blood:	n/a	n/a
41	POLR2A	chr2:182321198-182323193	GM12891	blood:	n/a	n/a
42	REST	chr2:182321331-182323417	HL-60	blood:	n/a	chr2:182322865-182322883 chr2:182322752-182322762
43	WRNIP1	chr2:182322596-182323370	GM12878	blood:	n/a	n/a
44	NFATC1	chr2:182321163-182323095	GM12878	blood:	n/a	n/a
45	CTCF	chr2:182322740-182322890	AG04449	skin:	n/a	n/a
46	POLR2A	chr2:182321231-182323187	Raji	blood:	n/a	n/a
47	RUNX3	chr2:182321133-182323108	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:182322419-182322857	ProgFib	skin:	n/a	n/a
49	TAF1	chr2:182322719-182323039	GM12891	blood:	n/a	n/a
50	RELA	chr2:182321194-182323804	GM18505	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:182322749-182322799	LNCaP	prostate:	n/a
2	chr2:182322749-182322799	T-47D	breast:	n/a
3	chr2:182322749-182322799	PFSK-1	brain:	n/a
4	chr2:182322749-182322799	U87	brain:	n/a
5	chr2:182322749-182322799	HMEC	breast:	n/a
6	chr2:182322749-182322799	HL-60	blood:	n/a
7	chr2:182322749-182322799	HCPEpiC	choroid plexus:	n/a
8	chr2:182322749-182322799	H1-hESC	embryonic stem cell:	embryo
9	chr2:182322749-182322799	AG04449	skin:	fetal
10	chr2:182322749-182322799	HEEpiC	esophagus:	n/a
11	chr2:182322749-182322799	MCF10A-Er-Src	breast:	n/a
12	chr2:182322749-182322799	GM12892	blood:	n/a
13	chr2:182322749-182322799	HPAEpiC	pulmonary alveolar:	n/a
14	chr2:182322749-182322799	CMK	blood:	n/a
15	chr2:182322749-182322799	NHBE	bronchial:	n/a
16	chr2:182322749-182322799	AG09319	gingival:	n/a
17	chr2:182322749-182322799	Caco-2	colon:	n/a
18	chr2:182322749-182322799	GM19239	blood:	n/a
19	chr2:182322749-182322799	NH-A	brain:	n/a
20	chr2:182322749-182322799	HepG2	liver:	n/a
21	chr2:182322749-182322799	HCM	heart:	n/a
22	chr2:182322749-182322799	GM12878	blood:	n/a
23	chr2:182322749-182322799	HRCEpiC	kidney:	n/a
24	chr2:182322749-182322799	BJ	skin:	n/a
25	chr2:182322749-182322799	A549	lung:	n/a
26	chr2:182322749-182322799	NB4	blood:	n/a
27	chr2:182322749-182322799	ProgFib	skin:	n/a
28	chr2:182322749-182322799	GM06990	blood:	n/a
29	chr2:182322749-182322799	HCT-116	colon:	n/a
30	chr2:182322749-182322799	AG04450	lung:	fetal
31	chr2:182322749-182322799	PrEC	prostate:	n/a
32	chr2:182322749-182322799	AoSMC	blood vessel:	n/a
33	chr2:182322749-182322799	SK-N-SH	brain:	n/a
34	chr2:182322749-182322799	Hepatocyte	liver:	n/a
35	chr2:182322749-182322799	HRE	kidney:	n/a
36	chr2:182322749-182322799	HCF	heart:	n/a
37	chr2:182322749-182322799	Hela-S3	cervix:	n/a
38	chr2:182322749-182322799	RPTEC	kidney:	n/a
39	chr2:182322749-182322799	ECC-1	luminal epithelium:	n/a
40	chr2:182322749-182322799	HEK293	kidney:	embryo
41	chr2:182322749-182322799	MCF-7	breast:	n/a
42	chr2:182322749-182322799	GM12891	blood:	n/a
43	chr2:182322749-182322799	NT2-D1	testis:	n/a
44	chr2:182322749-182322799	Jurkat	blood:	n/a
45	chr2:182322749-182322799	AG10803	skin:	n/a
46	chr2:182322749-182322799	HAEpiC	amniotic membrane:	n/a
47	chr2:182322749-182322799	SAEC	small airway:	n/a
48	chr2:182322749-182322799	SKMC	muscle:	n/a
49	chr2:182322749-182322799	HIPEpiC	eye:	n/a
50	chr2:182322749-182322799	K562	blood:	n/a

No data

Variant related genes	Relation type
ITGA4	TF binding region
ITGA4	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10153755	1.00[AMR][1000 genomes]
rs10180793	1.00[AMR][1000 genomes]
rs10206693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1026401	1.00[AMR][1000 genomes]
rs1037623	1.00[AMR][1000 genomes]
rs13415157	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13424840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1348124	1.00[AMR][1000 genomes]
rs1375489	1.00[AMR][1000 genomes]
rs1449258	1.00[AMR][1000 genomes]
rs1466110	1.00[AMR][1000 genomes]
rs155117	1.00[AMR][1000 genomes]
rs155118	1.00[AMR][1000 genomes]
rs2198730	1.00[AMR][1000 genomes]
rs2368214	1.00[AMR][1000 genomes]
rs3863936	1.00[AMR][1000 genomes]
rs3910673	1.00[AMR][1000 genomes]
rs4404231	1.00[AMR][1000 genomes]
rs57055225	1.00[AMR][1000 genomes]
rs6706626	1.00[AMR][1000 genomes]
rs6730994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73974897	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv834476	chr2:182179249-182360259	Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr2:182321200-182322800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:182321200-182323000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr2:182321200-182323200	Enhancers	Fetal Heart	heart
4	chr2:182321200-182323400	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr2:182321200-182327000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:182321400-182322800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr2:182321400-182323000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:182321400-182323200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:182321400-182323200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:182321400-182323200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:182321400-182323200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:182321400-182323200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:182321400-182323200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
14	chr2:182321400-182326600	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr2:182321600-182322800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:182321600-182322800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:182321600-182322800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr2:182321600-182323000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr2:182321600-182323000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
20	chr2:182321600-182323000	Active TSS	Brain Substantia Nigra	brain
21	chr2:182321600-182323000	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
22	chr2:182321600-182323200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:182321600-182323200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr2:182321600-182323200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr2:182321600-182323200	Active TSS	Colon Smooth Muscle	Colon
26	chr2:182321600-182323200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr2:182321600-182323200	Flanking Active TSS	HMEC	breast
28	chr2:182321600-182323400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
29	chr2:182321600-182323600	Active TSS	HSMM	muscle
30	chr2:182321600-182324000	Active TSS	Right Atrium	heart
31	chr2:182321600-182324000	Active TSS	NHLF	lung
32	chr2:182321600-182324200	Active TSS	NHDF-Ad	bronchial
33	chr2:182321600-182324400	Active TSS	Small Intestine	intestine
34	chr2:182321600-182324600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:182321600-182324600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:182321600-182325600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:182321600-182325800	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr2:182321600-182325800	Active TSS	HSMMtube	muscle
39	chr2:182321600-182326200	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:182321600-182326200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:182321600-182327200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:182321600-182327400	Active TSS	Thymus	Thymus
43	chr2:182321800-182322800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:182321800-182322800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:182321800-182322800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:182321800-182323000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:182321800-182323000	Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:182321800-182323000	Flanking Active TSS	Liver	Liver
49	chr2:182321800-182323000	Flanking Active TSS	Lung	lung
50	chr2:182321800-182323000	Flanking Active TSS	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links