Variant report

Variant	rs870486
Chromosome Location	chr1:223525848-223525849
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223519202..223521587-chr1:223525632..223530010,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10495207	0.88[EUR][1000 genomes]
rs10907376	0.82[EUR][1000 genomes]
rs11261264	0.84[EUR][1000 genomes]
rs12123148	0.83[EUR][1000 genomes]
rs12140453	0.83[EUR][1000 genomes]
rs12564615	0.81[EUR][1000 genomes]
rs1547788	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1619227	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1713219	0.86[AMR][1000 genomes]
rs1713220	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17162008	0.88[EUR][1000 genomes]
rs17163824	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17163825	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17163827	0.84[EUR][1000 genomes]
rs17163828	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17163831	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17539583	0.84[EUR][1000 genomes]
rs17578168	0.84[EUR][1000 genomes]
rs17578203	0.88[EUR][1000 genomes]
rs1772280	0.83[EUR][1000 genomes]
rs2459849	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2487521	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2678377	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34150324	0.83[EUR][1000 genomes]
rs35318812	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61838234	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838235	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61838236	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838237	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838238	0.84[EUR][1000 genomes]
rs61838239	0.84[EUR][1000 genomes]
rs61838240	0.84[EUR][1000 genomes]
rs61838241	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838243	0.84[EUR][1000 genomes]
rs61838246	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61838249	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61838250	0.87[EUR][1000 genomes]
rs61838252	0.80[EUR][1000 genomes]
rs61839867	0.83[EUR][1000 genomes]
rs6604709	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536652	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541162	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7555607	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9442046	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs870486	SUSD4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223506600-223526000	Weak transcription	Esophagus	oesophagus
2	chr1:223511800-223527000	Enhancers	Fetal Heart	heart
3	chr1:223514000-223526200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:223514400-223535800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:223517600-223527400	Enhancers	Ovary	ovary
6	chr1:223525200-223526000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:223525200-223526600	Strong transcription	Primary T cells from cord blood	blood
8	chr1:223525200-223526800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:223525400-223526000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:223525800-223526400	Bivalent Enhancer	Brain Anterior Caudate	brain

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