Variant report

Variant	rs62135101
Chromosome Location	chr2:55450112-55450113
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	NR2F2	chr2:55450103-55451423	K562	blood:	n/a	n/a
2	TCF12	chr2:55449943-55450960	A549	lung:	n/a	n/a
3	JUN	chr2:55450073-55450273	K562	blood:	n/a	n/a
4	ZNF384	chr2:55449977-55450174	K562	blood:	n/a	n/a
5	MAX	chr2:55450078-55451038	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55449257..55451239-chr2:55511673..55514610,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227799	TF binding region
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10175803	0.81[AFR][1000 genomes]
rs10176835	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10179352	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10193886	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10200424	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10208867	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11125559	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13395515	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13420684	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13427699	0.83[AFR][1000 genomes]
rs1437390	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437393	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118284	0.83[AFR][1000 genomes]
rs6545477	0.82[AFR][1000 genomes]
rs6711753	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720077	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6727118	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6727131	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6747364	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6757361	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9677948	0.87[AFR][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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
2	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:55424600-55451200	Weak transcription	HepG2	liver
4	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
7	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
10	chr2:55432000-55451200	Weak transcription	Dnd41	blood
11	chr2:55433000-55450200	Weak transcription	Ovary	ovary
12	chr2:55444400-55450400	Weak transcription	Gastric	stomach
13	chr2:55446800-55450200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:55447800-55450400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:55448400-55450200	Weak transcription	Psoas Muscle	Psoas
16	chr2:55448800-55450200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:55449400-55450200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:55449400-55450200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:55449400-55450200	Weak transcription	HSMM	muscle
20	chr2:55449400-55450400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:55449400-55451200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55449600-55450200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:55449600-55451000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55449800-55450200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:55449800-55450200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:55449800-55450200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr2:55449800-55450200	Enhancers	Fetal Lung	lung
28	chr2:55449800-55450200	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:55449800-55450200	Enhancers	Fetal Thymus	thymus
30	chr2:55449800-55450200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr2:55449800-55450200	Enhancers	Small Intestine	intestine
32	chr2:55449800-55450200	Enhancers	Thymus	Thymus
33	chr2:55449800-55450400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:55449800-55450400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:55450000-55450200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55450000-55450200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:55450000-55450200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr2:55450000-55450200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr2:55450000-55450200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr2:55450000-55450200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:55450000-55450200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:55450000-55450200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:55450000-55450200	Enhancers	Adipose Nuclei	Adipose
44	chr2:55450000-55450200	Enhancers	Liver	Liver
45	chr2:55450000-55450200	Enhancers	Brain Angular Gyrus	brain
46	chr2:55450000-55450200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr2:55450000-55450200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55450000-55450200	Enhancers	Fetal Stomach	stomach
49	chr2:55450000-55450200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:55450000-55450200	Flanking Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links