Variant report

Variant	rs2588514
Chromosome Location	chr2:55209177-55209178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55200821..55203664-chr2:55208517..55210374,2	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10174838	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10210840	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12464070	0.83[ASN][1000 genomes]
rs12477711	0.85[ASN][1000 genomes]
rs12713284	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13387751	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2015919	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2044291	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255112	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2580764	0.82[ASN][1000 genomes]
rs2580765	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2580772	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2580773	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2580776	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2588510	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2588517	0.81[ASN][1000 genomes]
rs2588518	0.89[ASN][1000 genomes]
rs2588521	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2860453	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2902649	0.85[ASN][1000 genomes]
rs2919129	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920893	0.85[AMR][1000 genomes]
rs2968787	0.82[ASN][1000 genomes]
rs2972097	0.82[ASN][1000 genomes]
rs35631428	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35826668	0.89[ASN][1000 genomes]
rs3806570	0.88[ASN][1000 genomes]
rs4672005	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545466	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6726158	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6755468	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6760429	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7340476	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562292	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584430	0.81[AMR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2588514	RTN4	cis	Whole Blood	GTEx
rs2588514	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2588514	RTN4	cis	Nerve Tibial	GTEx
rs2588514	RTN4	cis	Stomach	GTEx
rs2588514	RTN4	cis	Artery Tibial	GTEx
rs2588514	RTN4	cis	Thyroid	GTEx
rs2588514	RTN4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55193400-55214800	Strong transcription	HepG2	liver
5	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:55195000-55215200	Strong transcription	Dnd41	blood
9	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
13	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55198600-55215200	Weak transcription	Lung	lung
18	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:55200200-55209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
22	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
23	chr2:55203800-55210000	Weak transcription	Ovary	ovary
24	chr2:55203800-55210800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
26	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
27	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
28	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
29	chr2:55204600-55209400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:55204600-55210600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:55204800-55210400	Strong transcription	Osteobl	bone
32	chr2:55204800-55211600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:55205000-55211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:55205200-55210600	Weak transcription	Aorta	Aorta
35	chr2:55205200-55210600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:55205200-55213400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:55205200-55213600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:55205200-55214600	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:55205200-55214600	Weak transcription	Right Atrium	heart
40	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
41	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
42	chr2:55205600-55211000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:55205600-55214800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:55205800-55211800	Weak transcription	Fetal Stomach	stomach
45	chr2:55205800-55216000	Weak transcription	Fetal Intestine Small	intestine
46	chr2:55206200-55213000	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:55206400-55209600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55206400-55210400	Genic enhancers	NHEK	skin
49	chr2:55206400-55214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:55206600-55214000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links