Variant report

Variant	rs60866242
Chromosome Location	chr2:48059159-48059160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48036517..48039271-chr2:48058001..48060870,2	MCF-7	breast:
2	chr2:48009852..48011879-chr2:48057510..48059313,2	K562	blood:

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495947	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17036996	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17037002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17037018	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17037038	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2134056	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60154625	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704872	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6714441	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6723441	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73929251	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7572674	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv963230	chr2:48057165-48059438	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:48021400-48067600	Strong transcription	Dnd41	blood
3	chr2:48021600-48067000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:48023200-48065000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:48030200-48067600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:48030400-48067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:48030800-48067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:48030800-48067000	Strong transcription	Fetal Thymus	thymus
9	chr2:48031000-48067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:48031000-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:48031000-48067200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:48031200-48065800	Strong transcription	Liver	Liver
13	chr2:48031200-48066800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:48031400-48060600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:48031400-48066800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:48031400-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:48031400-48067800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:48031400-48067800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:48031400-48072600	Weak transcription	Stomach Mucosa	stomach
20	chr2:48032200-48067000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:48032400-48066800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:48032400-48068400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:48033600-48067000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:48033800-48067400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:48036000-48067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:48038000-48061200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:48038200-48071400	Weak transcription	Fetal Heart	heart
28	chr2:48038400-48066600	Strong transcription	Adipose Nuclei	Adipose
29	chr2:48039800-48059600	Weak transcription	Psoas Muscle	Psoas
30	chr2:48040400-48068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:48042000-48067800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:48043200-48066800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:48043400-48088600	Weak transcription	Pancreas	Pancrea
34	chr2:48043600-48060800	Weak transcription	Esophagus	oesophagus
35	chr2:48043600-48067000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:48044800-48071000	Weak transcription	Fetal Brain Male	brain
37	chr2:48045000-48059400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:48045800-48071600	Weak transcription	Aorta	Aorta
39	chr2:48047800-48067400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:48048200-48061800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:48048200-48072400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:48048400-48070000	Weak transcription	Small Intestine	intestine
43	chr2:48048600-48062200	Weak transcription	Brain Angular Gyrus	brain
44	chr2:48048600-48063200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:48048600-48080600	Weak transcription	NHLF	lung
46	chr2:48049200-48062200	Weak transcription	HSMMtube	muscle
47	chr2:48049200-48063200	Weak transcription	Colonic Mucosa	Colon
48	chr2:48049200-48070000	Weak transcription	Brain Substantia Nigra	brain
49	chr2:48049200-48096000	Weak transcription	Gastric	stomach
50	chr2:48049400-48059600	Weak transcription	Brain Hippocampus Middle	brain

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