Variant report

Variant	rs60339919
Chromosome Location	chr3:160399012-160399013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10460866	0.89[EUR][1000 genomes]
rs11714916	0.80[EUR][1000 genomes]
rs11720693	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062928	0.91[EUR][1000 genomes]
rs13072556	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075424	0.86[EUR][1000 genomes]
rs13085507	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1403045	0.80[EUR][1000 genomes]
rs1882125	0.88[EUR][1000 genomes]
rs2367209	0.93[EUR][1000 genomes]
rs34058107	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34444753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498840	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57718211	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6792943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806755	0.80[EUR][1000 genomes]
rs71314011	0.89[EUR][1000 genomes]
rs7633839	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634255	0.88[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60339919	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160395600-160401600	Weak transcription	Gastric	stomach
2	chr3:160395600-160401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:160395800-160400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:160397000-160412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:160397200-160401800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:160397400-160400800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:160397400-160401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:160397400-160401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:160397400-160401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160397400-160403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:160397600-160401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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