Variant report

Variant	rs2968787
Chromosome Location	chr2:55265785-55265786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55265645..55268025-chr2:55268205..55270605,2	MCF-7	breast:
2	chr2:55255745..55260236-chr2:55263069..55266549,5	K562	blood:
3	chr2:55253298..55255265-chr2:55265294..55267097,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10174838	0.88[ASN][1000 genomes]
rs10210840	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12464070	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12477711	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713284	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13387751	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2015919	0.81[ASN][1000 genomes]
rs2044291	0.95[ASN][1000 genomes]
rs2255112	1.00[JPT][hapmap]
rs2255393	0.90[JPT][hapmap]
rs2580765	1.00[JPT][hapmap]
rs2580772	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2580776	0.85[ASN][1000 genomes]
rs2588510	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2588514	0.82[ASN][1000 genomes]
rs2588517	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs2588518	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2588519	0.86[JPT][hapmap]
rs2588521	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2860453	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2902649	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2919129	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2920878	0.81[CEU][hapmap]
rs2920893	0.95[ASN][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2968794	0.81[CEU][hapmap]
rs2968795	0.81[CEU][hapmap]
rs2968804	0.86[JPT][hapmap]
rs2972075	0.80[CEU][hapmap]
rs2972090	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs2972097	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35631428	0.92[ASN][1000 genomes]
rs35826668	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3806570	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4672005	0.95[ASN][1000 genomes]
rs6545466	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6713935	0.83[YRI][hapmap]
rs6726158	0.87[ASN][1000 genomes]
rs6755468	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6760429	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7340476	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7562292	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7570629	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7584430	0.81[ASN][1000 genomes]
rs968998	0.87[CHB][hapmap];0.82[ASN][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	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
2	esv2474783	chr2:55265536-55266830	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2968787	RTN4	cis	Artery Aorta	GTEx
rs2968787	RTN4	cis	Adipose Subcutaneous	GTEx
rs2968787	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2968787	RTN4	cis	Artery Tibial	GTEx
rs2968787	RTN4	cis	Nerve Tibial	GTEx
rs2968787	RTN4	cis	Esophagus Mucosa	GTEx
rs2968787	RTN4	cis	Whole Blood	GTEx
rs2968787	RTN4	cis	Esophagus Muscularis	GTEx
rs2968787	RTN4	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
2	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
3	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
5	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:55254200-55269800	Weak transcription	Aorta	Aorta
7	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:55255400-55272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55255400-55272600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:55256400-55266600	Weak transcription	Left Ventricle	heart
11	chr2:55256400-55270400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:55259000-55267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:55259000-55272800	Weak transcription	Small Intestine	intestine
14	chr2:55259200-55272800	Weak transcription	Fetal Heart	heart
15	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
16	chr2:55260800-55266000	Weak transcription	Adipose Nuclei	Adipose
17	chr2:55260800-55266200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:55260800-55266600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:55260800-55270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:55260800-55271200	Weak transcription	Lung	lung
21	chr2:55260800-55271200	Weak transcription	Right Atrium	heart
22	chr2:55260800-55272000	Weak transcription	NH-A	brain
23	chr2:55260800-55272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:55260800-55273200	Weak transcription	Psoas Muscle	Psoas
25	chr2:55261200-55273000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:55261400-55272800	Weak transcription	Thymus	Thymus
27	chr2:55261600-55265800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:55261600-55266000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:55261600-55266000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:55261600-55266200	Weak transcription	Brain Angular Gyrus	brain
31	chr2:55261600-55266600	Weak transcription	Fetal Thymus	thymus
32	chr2:55261600-55269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:55261600-55271200	Weak transcription	Ovary	ovary
34	chr2:55262000-55266600	ZNF genes & repeats	A549	lung
35	chr2:55262600-55270200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:55262800-55267600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:55263000-55266000	Weak transcription	Hela-S3	cervix
38	chr2:55263800-55266200	Genic enhancers	Muscle Satellite Cultured Cells	--
39	chr2:55263800-55266800	ZNF genes & repeats	GM12878-XiMat	blood
40	chr2:55263800-55267200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:55264000-55266200	Enhancers	HepG2	liver
42	chr2:55264200-55265800	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:55264200-55267600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:55264400-55266200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr2:55264600-55265800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:55264600-55265800	Enhancers	HMEC	breast
47	chr2:55264600-55266200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr2:55264600-55266400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55264600-55267200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:55264600-55268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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