Variant report

Variant	rs173555
Chromosome Location	chr5:126528653-126528654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10035217	0.85[EUR][1000 genomes]
rs10037625	0.84[EUR][1000 genomes]
rs10038644	0.91[EUR][1000 genomes]
rs10041457	0.91[EUR][1000 genomes]
rs1004500	0.85[EUR][1000 genomes]
rs10062622	0.88[EUR][1000 genomes]
rs10067364	0.84[CEU][hapmap]
rs1013662	0.81[CEU][hapmap]
rs108558	0.85[EUR][1000 genomes]
rs11960799	0.84[CEU][hapmap]
rs12515192	0.84[CEU][hapmap]
rs12655640	0.84[CEU][hapmap]
rs13178353	0.88[EUR][1000 genomes]
rs13190493	0.91[EUR][1000 genomes]
rs1543815	0.90[EUR][1000 genomes]
rs1860439	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860440	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1860441	0.95[EUR][1000 genomes]
rs193712	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041318	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs2109215	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs2191209	0.89[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs2408788	0.90[EUR][1000 genomes]
rs2408789	0.90[EUR][1000 genomes]
rs2436437	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248040	0.85[CEU][hapmap];0.91[JPT][hapmap]
rs248042	0.95[EUR][1000 genomes]
rs248062	0.82[EUR][1000 genomes]
rs248081	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs248091	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248092	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs248093	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248094	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248095	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248096	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248101	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs248102	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248104	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248105	0.86[EUR][1000 genomes]
rs248106	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248107	0.96[CEU][hapmap];0.96[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248108	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248109	0.85[EUR][1000 genomes]
rs248111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248112	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248113	0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs248114	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248115	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248116	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248117	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248118	0.86[EUR][1000 genomes]
rs248119	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248121	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248122	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248124	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248125	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248126	0.85[EUR][1000 genomes]
rs248127	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248128	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248129	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248131	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532882	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585204	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2898037	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095137	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3097870	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915634	0.81[EUR][1000 genomes]
rs3936304	0.89[EUR][1000 genomes]
rs3936305	0.89[EUR][1000 genomes]
rs4455612	0.90[EUR][1000 genomes]
rs4835925	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4836310	0.91[EUR][1000 genomes]
rs4836313	0.92[EUR][1000 genomes]
rs4836315	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57555006	0.84[EUR][1000 genomes]
rs62374042	0.82[EUR][1000 genomes]
rs6859327	0.83[AFR][1000 genomes]
rs6864668	0.84[EUR][1000 genomes]
rs6873502	0.91[EUR][1000 genomes]
rs6875043	0.89[EUR][1000 genomes]
rs6879393	0.84[EUR][1000 genomes]
rs6881948	0.91[EUR][1000 genomes]
rs6883106	0.90[EUR][1000 genomes]
rs6883627	0.91[EUR][1000 genomes]
rs6883871	0.84[CEU][hapmap]
rs6884988	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6887929	0.91[EUR][1000 genomes]
rs6888087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6891436	0.84[CEU][hapmap]
rs726990	0.85[EUR][1000 genomes]
rs727038	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs729607	0.84[CEU][hapmap]
rs7700812	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706333	0.84[CEU][hapmap]
rs7713933	0.80[CEU][hapmap]
rs7731621	0.93[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs7734890	0.92[EUR][1000 genomes]
rs7736693	0.84[CEU][hapmap]
rs885699	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327428	0.84[CEU][hapmap]
rs9687751	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9687752	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9763733	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs990743	0.88[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	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs173555	MARCH3	cis	Muscle Skeletal	GTEx
rs173555	C5orf63	cis	Artery Aorta	GTEx
rs173555	C5orf63	cis	Artery Tibial	GTEx
rs173555	C5orf63	cis	Nerve Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126528200-126528800	Enhancers	HSMM	muscle
2	chr5:126528200-126529600	Enhancers	Fetal Intestine Small	intestine
3	chr5:126528200-126529800	Enhancers	Fetal Intestine Large	intestine
4	chr5:126528200-126530000	Enhancers	Stomach Mucosa	stomach
5	chr5:126528400-126529200	Enhancers	HSMMtube	muscle
6	chr5:126528600-126528800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:126528600-126529000	Enhancers	NH-A	brain
8	chr5:126528600-126529200	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links