Variant report

Variant	rs2968793
Chromosome Location	chr2:55285024-55285025
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	chr2:55276015..55279401-chr2:55283233..55288147,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10174838	0.85[EUR][1000 genomes]
rs10210840	0.84[EUR][1000 genomes]
rs11674808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713284	0.87[EUR][1000 genomes]
rs13011689	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387751	0.85[EUR][1000 genomes]
rs2044291	0.85[EUR][1000 genomes]
rs2580772	0.83[EUR][1000 genomes]
rs2580776	0.83[EUR][1000 genomes]
rs2860453	0.87[EUR][1000 genomes]
rs2919129	0.83[EUR][1000 genomes]
rs2920862	0.86[ASN][1000 genomes]
rs2920878	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920893	0.87[EUR][1000 genomes]
rs2920900	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968786	0.87[EUR][1000 genomes]
rs2968790	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968794	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2968795	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968798	0.86[ASN][1000 genomes]
rs2968822	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968825	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968827	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972070	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972071	0.86[ASN][1000 genomes]
rs2972072	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972075	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972097	0.88[EUR][1000 genomes]
rs35631428	0.85[EUR][1000 genomes]
rs4672005	0.85[EUR][1000 genomes]
rs6545466	0.87[EUR][1000 genomes]
rs6726158	0.86[EUR][1000 genomes]
rs6755468	0.85[EUR][1000 genomes]
rs6760429	0.87[EUR][1000 genomes]
rs7340476	0.85[EUR][1000 genomes]
rs7562292	0.87[EUR][1000 genomes]
rs7584430	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2968793	RTN4	cis	Nerve Tibial	GTEx
rs2968793	RTN4	cis	Thyroid	GTEx
rs2968793	RTN4	cis	Whole Blood	GTEx
rs2968793	RTN4	cis	Adipose Subcutaneous	GTEx
rs2968793	RTN4	cis	Artery Tibial	GTEx
rs2968793	RTN4	cis	Artery Aorta	GTEx
rs2968793	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2968793	RTN4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55278200-55288800	Weak transcription	Lung	lung
2	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:55279800-55287400	Weak transcription	HSMM	muscle
8	chr2:55280000-55289000	Weak transcription	HepG2	liver
9	chr2:55280200-55287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:55280200-55288200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:55281800-55287600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:55283600-55285200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:55283600-55287600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:55283800-55286600	Weak transcription	K562	blood
15	chr2:55284800-55287200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links