Variant report

Variant	rs564883
Chromosome Location	chr1:160732784-160732785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11265473	0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11582702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12064520	0.87[EUR][1000 genomes]
rs12068654	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12082740	0.97[EUR][1000 genomes]
rs1328111	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17313062	0.81[EUR][1000 genomes]
rs2176873	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766370	0.86[MEX][hapmap]
rs3766374	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs477299	0.86[EUR][1000 genomes]
rs504170	0.87[EUR][1000 genomes]
rs518242	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs528095	0.87[EUR][1000 genomes]
rs546757	0.87[EUR][1000 genomes]
rs564833	0.87[EUR][1000 genomes]
rs574491	0.87[EUR][1000 genomes]
rs579821	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs564883	RXFP4	cis	parietal	SCAN
rs564883	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs564883	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160722000-160736400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:160730000-160736400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160730000-160736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:160731200-160733800	Enhancers	NHEK	skin
5	chr1:160731400-160736600	Weak transcription	Esophagus	oesophagus
6	chr1:160731600-160733800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:160732200-160737200	Weak transcription	HMEC	breast
8	chr1:160732400-160736600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:160732400-160736600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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