Variant report

Variant	rs2658973
Chromosome Location	chr12:45269640-45269641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr12:45269018-45270675	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr12:45269089-45269672	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr12:45268863-45270739	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:45269407-45270406	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:45268975-45270442	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZBTB7A	chr12:45269031-45271159	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
7	ZBTB7A	chr12:45268901-45271105	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
8	POLR2A	chr12:45269560-45270774	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr12:45268594-45271198	SK-N-SH	brain:	n/a	n/a
10	REST	chr12:45269036-45271162	H1-neurons	neurons:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
11	TAF1	chr12:45269354-45269701	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr12:45269500-45269650	SK-N-SH_RA	brain:	n/a	n/a
13	GATA2	chr12:45268654-45269926	SH-SY5Y	brain:	n/a	chr12:45268852-45268860
14	POLR2A	chr12:45269185-45270789	H1-neurons	neurons:	n/a	n/a
15	MAX	chr12:45269268-45271034	ECC-1	luminal epithelium:	n/a	n/a
16	SIN3A	chr12:45268716-45271054	H1-hESC	embryonic stem cell:	n/a	chr12:45269887-45269898 chr12:45270781-45270789 chr12:45268990-45269004
17	MAX	chr12:45269390-45269916	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:45269448-45269665	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr12:45269216-45271039	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr12:45268740-45270705	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr12:45269235-45269994	H1-hESC	embryonic stem cell:	n/a	chr12:45269727-45269734 chr12:45269727-45269734 chr12:45269726-45269734 chr12:45269727-45269734
22	ZNF263	chr12:45268711-45269924	HEK293-T-REx	kidney:	n/a	chr12:45269265-45269274
23	CHD1	chr12:45268922-45269885	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:45269604-45269654	BE2_C	brain:	n/a
2	chr12:45269604-45269654	PANC-1	pancreas:	n/a
3	chr12:45269604-45269654	CMK	blood:	n/a
4	chr12:45269610-45269660	HEEpiC	esophagus:	n/a
5	chr12:45269610-45269660	HIPEpiC	eye:	n/a
6	chr12:45269610-45269660	HNPCEpiC	eye:	n/a
7	chr12:45269610-45269660	GM12878	blood:	n/a
8	chr12:45269604-45269654	IMR90	lung:	fetal
9	chr12:45269604-45269654	GM06990	blood:	n/a
10	chr12:45269604-45269654	AG04449	skin:	fetal
11	chr12:45269604-45269654	NHBE	bronchial:	n/a
12	chr12:45269604-45269654	GM12878	blood:	n/a
13	chr12:45269610-45269660	HRPEpiC	eye:	n/a
14	chr12:45269610-45269660	ProgFib	skin:	n/a
15	chr12:45269604-45269654	Jurkat	blood:	n/a
16	chr12:45269610-45269660	HCPEpiC	choroid plexus:	n/a
17	chr12:45269604-45269654	HCPEpiC	choroid plexus:	n/a
18	chr12:45269604-45269654	RPTEC	kidney:	n/a
19	chr12:45269604-45269654	HRPEpiC	eye:	n/a
20	chr12:45269610-45269660	GM19239	blood:	n/a
21	chr12:45269610-45269660	HRCEpiC	kidney:	n/a
22	chr12:45269604-45269654	PFSK-1	brain:	n/a
23	chr12:45269604-45269654	HL-60	blood:	n/a
24	chr12:45269610-45269660	U87	brain:	n/a
25	chr12:45269610-45269660	K562	blood:	n/a
26	chr12:45269604-45269654	SK-N-SH	brain:	n/a
27	chr12:45269610-45269660	NHBE	bronchial:	n/a
28	chr12:45269604-45269654	AG09319	gingival:	n/a
29	chr12:45269610-45269660	NH-A	brain:	n/a
30	chr12:45269610-45269660	SK-N-MC	brain:	n/a
31	chr12:45269604-45269654	HMEC	breast:	n/a
32	chr12:45269610-45269660	ECC-1	luminal epithelium:	n/a
33	chr12:45269610-45269660	GM12892	blood:	n/a
34	chr12:45269610-45269660	HCF	heart:	n/a
35	chr12:45269604-45269654	GM19239	blood:	n/a
36	chr12:45269604-45269654	HAEpiC	amniotic membrane:	n/a
37	chr12:45269610-45269660	SKMC	muscle:	n/a
38	chr12:45269610-45269660	BJ	skin:	n/a
39	chr12:45269604-45269654	ovcar-3	ovarian:	n/a
40	chr12:45269604-45269654	ProgFib	skin:	n/a
41	chr12:45269610-45269660	T-47D	breast:	n/a
42	chr12:45269610-45269660	Hepatocyte	liver:	n/a
43	chr12:45269610-45269660	NT2-D1	testis:	n/a
44	chr12:45269604-45269654	BJ	skin:	n/a
45	chr12:45269604-45269654	LNCaP	prostate:	n/a
46	chr12:45269610-45269660	HEK293	kidney:	embryo
47	chr12:45269604-45269654	HCF	heart:	n/a
48	chr12:45269610-45269660	PrEC	prostate:	n/a
49	chr12:45269604-45269654	HEEpiC	esophagus:	n/a
50	chr12:45269604-45269654	GM12891	blood:	n/a

No data

Variant related genes	Relation type
NELL2	TF binding region
NELL2	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10736022	1.00[AFR][1000 genomes]
rs1224443	1.00[YRI][hapmap]
rs1376125	0.84[AFR][1000 genomes]
rs1450550	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.80[AFR][1000 genomes]
rs1964487	1.00[AFR][1000 genomes]
rs2658953	0.96[AFR][1000 genomes]
rs2658962	1.00[AFR][1000 genomes]
rs2658968	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2658974	1.00[AFR][1000 genomes]
rs2703039	1.00[AFR][1000 genomes]
rs2703041	1.00[AFR][1000 genomes]
rs2703045	1.00[AFR][1000 genomes]
rs2710426	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2710456	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs376283	0.83[MKK][hapmap]
rs421642	1.00[ASW][hapmap]
rs4257041	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4306333	1.00[AFR][1000 genomes]
rs7132477	1.00[AFR][1000 genomes]
rs7964617	1.00[AFR][1000 genomes]
rs7964721	1.00[AFR][1000 genomes]
rs7968547	1.00[AFR][1000 genomes]
rs978696	0.83[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
2	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45264800-45271200	Active TSS	Fetal Brain Male	brain
2	chr12:45266000-45270600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr12:45266800-45270800	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr12:45267200-45271000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45267200-45271400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:45267800-45271000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr12:45268000-45270000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr12:45268000-45270800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:45268000-45270800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:45268000-45271000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:45268000-45271200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:45268200-45271200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:45268600-45269800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:45268600-45270000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
15	chr12:45268600-45270400	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr12:45268600-45270400	Active TSS	Right Atrium	heart
17	chr12:45268600-45270600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:45268600-45271000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:45268600-45271200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr12:45268800-45269800	Enhancers	Lung	lung
25	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
27	chr12:45268800-45269800	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr12:45268800-45269800	Enhancers	Spleen	Spleen
29	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
30	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:45268800-45270000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	NHEK	skin
36	chr12:45268800-45270800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:45268800-45270800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:45268800-45271000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:45268800-45271000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr12:45268800-45271200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:45268800-45271200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:45268800-45271200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:45269000-45269800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:45269000-45269800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:45269000-45269800	Flanking Bivalent TSS/Enh	Liver	Liver
46	chr12:45269000-45270000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
47	chr12:45269000-45270000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
48	chr12:45269000-45270000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:45269000-45270000	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr12:45269000-45270000	Flanking Bivalent TSS/Enh	NH-A	brain

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