Variant report

Variant	rs4672006
Chromosome Location	chr2:55251511-55251512
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55245011..55247166-chr2:55250682..55252602,2	MCF-7	breast:
2	chr2:55243166..55246645-chr2:55249862..55254918,6	K562	blood:
3	chr2:55248265..55251849-chr2:55275117..55277756,4	MCF-7	breast:
4	chr2:55251258..55253325-chr2:55261770..55263673,2	K562	blood:
5	chr2:55238125..55242197-chr2:55249599..55253048,4	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1012603	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10496034	0.84[EUR][1000 genomes]
rs10496040	0.80[EUR][1000 genomes]
rs17046514	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17046518	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17046583	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17046643	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17046658	0.80[EUR][1000 genomes]
rs2028728	0.90[EUR][1000 genomes]
rs2241958	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2255026	0.83[AFR][1000 genomes]
rs2580771	0.83[AFR][1000 genomes]
rs2588515	0.83[AFR][1000 genomes]
rs2588516	0.83[AFR][1000 genomes]
rs2588522	0.83[AFR][1000 genomes]
rs2919126	0.83[AFR][1000 genomes]
rs34378852	0.83[AFR][1000 genomes]
rs4233955	0.84[EUR][1000 genomes]
rs4671993	0.82[EUR][1000 genomes]
rs4671995	0.84[EUR][1000 genomes]
rs4671997	0.84[EUR][1000 genomes]
rs4672009	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57737203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60553807	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545464	0.83[AFR][1000 genomes]
rs6734314	0.83[AFR][1000 genomes]
rs6739210	0.83[AFR][1000 genomes]
rs73936818	0.90[EUR][1000 genomes]
rs73936829	0.80[EUR][1000 genomes]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672006	RTN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
5	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
6	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
8	chr2:55241400-55253400	Weak transcription	Fetal Lung	lung
9	chr2:55242000-55252400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:55242200-55253400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:55242400-55253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
14	chr2:55243200-55252600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55245000-55256000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:55245400-55253400	Weak transcription	Liver	Liver
18	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
19	chr2:55246400-55254000	Enhancers	Brain Substantia Nigra	brain
20	chr2:55246800-55251600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:55246800-55259800	Weak transcription	NH-A	brain
22	chr2:55247200-55252200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:55247400-55252200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:55247600-55251600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:55247800-55251600	Genic enhancers	K562	blood
26	chr2:55248200-55252200	Enhancers	HUVEC	blood vessel
27	chr2:55248200-55253200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:55248200-55253600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:55248200-55253800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:55248200-55255200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:55248200-55255200	Weak transcription	Left Ventricle	heart
32	chr2:55248200-55258400	Weak transcription	Lung	lung
33	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:55248600-55251600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:55248600-55251600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr2:55248600-55256400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr2:55248800-55252200	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:55249000-55252000	Weak transcription	Fetal Brain Female	brain
39	chr2:55249000-55256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:55249000-55256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:55249000-55256600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:55249000-55256600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:55249000-55256600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:55249200-55251800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:55249200-55252200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:55249200-55255000	Strong transcription	Dnd41	blood
47	chr2:55249200-55256600	Enhancers	Brain Angular Gyrus	brain
48	chr2:55249400-55251600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:55249400-55253000	Enhancers	NHLF	lung
50	chr2:55249400-55253600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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