Variant report

Variant	rs11884960
Chromosome Location	chr2:182549596-182549597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:182549531-182550782	HL-60	blood:	n/a	chr2:182549831-182549840
2	BCL3	chr2:182549472-182549836	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:182549480-182550456	H1-neurons	neurons:	n/a	n/a
4	REST	chr2:182549576-182550734	ECC-1	luminal epithelium:	n/a	chr2:182549831-182549840
5	PBX3	chr2:182549505-182549756	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:182549441-182550206	H1-neurons	neurons:	n/a	n/a
7	STAT5A	chr2:182549412-182549890	GM12878	blood:	n/a	chr2:182549582-182549590
8	NFATC1	chr2:182549462-182549832	GM12878	blood:	n/a	n/a
9	REST	chr2:182549555-182550492	PFSK-1	brain:	n/a	chr2:182549831-182549840
10	REST	chr2:182549236-182550562	PFSK-1	brain:	n/a	chr2:182549831-182549840
11	BCL3	chr2:182549400-182549853	GM12878	blood:	n/a	chr2:182549831-182549840
12	CHD2	chr2:182549587-182549690	HepG2	liver:	n/a	n/a
13	SUZ12	chr2:182546965-182550375	H1-hESC	embryonic stem cell:	n/a	n/a
14	SUZ12	chr2:182543491-182550280	NT2-D1	testis:	n/a	n/a
15	NFATC1	chr2:182549437-182549954	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:182549565-182549615	GM12878	blood:	n/a
2	chr2:182549565-182549615	AG09309	skin:	n/a
3	chr2:182549565-182549615	Hela-S3	cervix:	n/a
4	chr2:182549565-182549615	IMR90	lung:	fetal
5	chr2:182549565-182549615	NHDF-neo	bronchial:	n/a
6	chr2:182549565-182549615	RPTEC	kidney:	n/a
7	chr2:182549565-182549615	HCT-116	colon:	n/a
8	chr2:182549565-182549615	GM19239	blood:	n/a
9	chr2:182549565-182549615	HRPEpiC	eye:	n/a
10	chr2:182549565-182549615	H1-hESC	embryonic stem cell:	embryo
11	chr2:182549565-182549615	NHBE	bronchial:	n/a
12	chr2:182549565-182549615	SKMC	muscle:	n/a
13	chr2:182549565-182549615	MCF10A-Er-Src	breast:	n/a
14	chr2:182549565-182549615	NB4	blood:	n/a
15	chr2:182549565-182549615	HRE	kidney:	n/a
16	chr2:182549565-182549615	HepG2	liver:	n/a
17	chr2:182549565-182549615	SAEC	small airway:	n/a
18	chr2:182549565-182549615	AoSMC	blood vessel:	n/a
19	chr2:182549565-182549615	BJ	skin:	n/a
20	chr2:182549565-182549615	ovcar-3	ovarian:	n/a
21	chr2:182549565-182549615	GM12891	blood:	n/a
22	chr2:182549565-182549615	A549	lung:	n/a
23	chr2:182549565-182549615	PrEC	prostate:	n/a
24	chr2:182549565-182549615	HAEpiC	amniotic membrane:	n/a
25	chr2:182549565-182549615	Jurkat	blood:	n/a
26	chr2:182549565-182549615	ProgFib	skin:	n/a
27	chr2:182549565-182549615	CMK	blood:	n/a
28	chr2:182549565-182549615	GM06990	blood:	n/a
29	chr2:182549565-182549615	HNPCEpiC	eye:	n/a
30	chr2:182549565-182549615	HMEC	breast:	n/a
31	chr2:182549565-182549615	HIPEpiC	eye:	n/a
32	chr2:182549565-182549615	HCPEpiC	choroid plexus:	n/a
33	chr2:182549565-182549615	ECC-1	luminal epithelium:	n/a
34	chr2:182549565-182549615	Caco-2	colon:	n/a
35	chr2:182549565-182549615	MCF-7	breast:	n/a
36	chr2:182549565-182549615	SK-N-SH	brain:	n/a
37	chr2:182549565-182549615	PFSK-1	brain:	n/a
38	chr2:182549565-182549615	GM12892	blood:	n/a
39	chr2:182549565-182549615	Hepatocyte	liver:	n/a
40	chr2:182549565-182549615	AG04449	skin:	fetal
41	chr2:182549565-182549615	HRCEpiC	kidney:	n/a
42	chr2:182549565-182549615	HEEpiC	esophagus:	n/a
43	chr2:182549565-182549615	HCF	heart:	n/a
44	chr2:182549565-182549615	AG09319	gingival:	n/a
45	chr2:182549565-182549615	PANC-1	pancreas:	n/a
46	chr2:182549565-182549615	HL-60	blood:	n/a
47	chr2:182549565-182549615	HCM	heart:	n/a
48	chr2:182549565-182549615	K562	blood:	n/a
49	chr2:182549565-182549615	AG04450	lung:	fetal
50	chr2:182549565-182549615	HUVEC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:182544304..182548457-chr2:182549208..182552987,3	MCF-7	breast:
2	chr2:182546719..182548427-chr2:182548447..182551068,2	K562	blood:
3	chr2:182543026..182545649-chr2:182549552..182552304,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA4-1	chr2:182546597-182554169	NONHSAT075881

No data

Variant related genes	Relation type
CERKL	TF binding region
NEUROD1	TF binding region
CERKL	CpG island
NEUROD1	CpG island
ENSG00000188452	Chromatin interaction
ENSG00000234595	Chromatin interaction
ENSG00000162992	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1123253	1.00[AMR][1000 genomes]
rs12987928	1.00[AMR][1000 genomes]
rs2696356	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182543600-182550200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:182545200-182549800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:182545200-182550000	Bivalent Enhancer	Fetal Thymus	thymus
4	chr2:182545200-182550200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:182545200-182550400	Bivalent Enhancer	Fetal Brain Male	brain
6	chr2:182546000-182550200	Weak transcription	Gastric	stomach
7	chr2:182547000-182550200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr2:182547400-182550200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr2:182547400-182550400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr2:182547400-182550400	Bivalent Enhancer	Placenta	Placenta
11	chr2:182547600-182549800	Bivalent Enhancer	Lung	lung
12	chr2:182547600-182550200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:182547800-182549600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:182547800-182549600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:182548000-182549600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:182548000-182550200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
17	chr2:182548400-182549600	Bivalent Enhancer	Fetal Stomach	stomach
18	chr2:182548400-182549800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:182548600-182549600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
20	chr2:182548600-182550000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr2:182548600-182550000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
22	chr2:182548600-182550200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:182548800-182549600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
24	chr2:182548800-182550000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:182548800-182550000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:182548800-182550200	Enhancers	Pancreas	Pancrea
27	chr2:182549000-182549600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr2:182549000-182549800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:182549000-182550000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:182549000-182550000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:182549000-182550400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
32	chr2:182549200-182549600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:182549200-182549600	Bivalent Enhancer	Colon Smooth Muscle	Colon
34	chr2:182549200-182549600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr2:182549200-182550000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:182549200-182550000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
37	chr2:182549200-182550000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:182549200-182550000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:182549200-182550000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
40	chr2:182549200-182550200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:182549200-182550200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr2:182549200-182550200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:182549200-182550200	Bivalent Enhancer	Brain Germinal Matrix	brain
44	chr2:182549200-182550400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:182549200-182550600	Bivalent Enhancer	Fetal Brain Female	brain
46	chr2:182549400-182549600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
47	chr2:182549400-182549600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr2:182549400-182549600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr2:182549400-182549600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr2:182549400-182549600	Bivalent Enhancer	Colonic Mucosa	Colon

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