Variant report

Variant	rs4669517
Chromosome Location	chr2:10146963-10146964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:10146701-10147529	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr2:10146900-10147050	SK-N-SH_RA	brain:	n/a	n/a
3	GATA2	chr2:10146769-10147241	SH-SY5Y	brain:	n/a	n/a
4	GATA1	chr2:10146626-10147256	PBDE	blood:	n/a	n/a
5	REST	chr2:10146755-10147201	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr2:10146900-10147050	HRE	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000188525	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12470881	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477748	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34521538	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][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	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:10125000-10147600	Weak transcription	K562	blood
4	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
5	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:10134200-10147000	Weak transcription	HSMMtube	muscle
8	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:10137000-10148000	Weak transcription	Hela-S3	cervix
10	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:10139600-10147000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:10141000-10147000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:10142000-10147600	Weak transcription	HepG2	liver
16	chr2:10142400-10148200	Enhancers	Adipose Nuclei	Adipose
17	chr2:10142600-10147000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:10142800-10148000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:10143800-10147200	Weak transcription	Osteobl	bone
20	chr2:10144400-10147200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:10144800-10147200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:10145800-10151000	Enhancers	Pancreas	Pancrea
23	chr2:10146400-10147000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
24	chr2:10146400-10147000	Enhancers	Fetal Brain Male	brain
25	chr2:10146400-10147000	Active TSS	Fetal Brain Female	brain
26	chr2:10146400-10147000	Flanking Active TSS	Right Ventricle	heart
27	chr2:10146400-10147000	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr2:10146400-10147000	Enhancers	HUVEC	blood vessel
29	chr2:10146400-10147200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:10146400-10147200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr2:10146400-10147200	Enhancers	Ovary	ovary
32	chr2:10146400-10147400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:10146400-10147600	Enhancers	Left Ventricle	heart
34	chr2:10146400-10148000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:10146400-10148800	Enhancers	Liver	Liver
36	chr2:10146400-10148800	Enhancers	Gastric	stomach
37	chr2:10146400-10150800	Enhancers	Colon Smooth Muscle	Colon
38	chr2:10146400-10150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr2:10146400-10151200	Enhancers	Placenta	Placenta
40	chr2:10146600-10147000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:10146600-10147000	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr2:10146600-10147000	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:10146600-10147200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:10146600-10147200	Enhancers	NH-A	brain
45	chr2:10146600-10147400	Enhancers	Fetal Heart	heart
46	chr2:10146600-10147400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr2:10146600-10147800	Bivalent Enhancer	Colonic Mucosa	Colon
48	chr2:10146600-10148800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:10146600-10148800	Enhancers	Right Atrium	heart
50	chr2:10146800-10147000	Enhancers	H1 Cell Line	embryonic stem cell

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