Variant report

Variant	rs2099604
Chromosome Location	chr1:160505787-160505788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr1:160503536-160506269	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000234425	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1055880	0.86[CEU][hapmap]
rs1061217	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs10752638	0.83[EUR][1000 genomes]
rs10797073	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10797083	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10908789	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10908794	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10908796	0.83[EUR][1000 genomes]
rs11265442	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs11265452	0.91[CEU][hapmap]
rs1138323	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11583402	0.82[CEU][hapmap]
rs11585738	0.86[CEU][hapmap]
rs11590035	0.86[CEU][hapmap]
rs12144628	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402879	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12728784	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12736781	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1394078	0.82[CEU][hapmap]
rs1394079	0.86[CHB][hapmap]
rs151607	0.82[CEU][hapmap]
rs1572382	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1604783	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16832208	1.00[YRI][hapmap]
rs16832283	0.91[CEU][hapmap]
rs17381453	0.86[CEU][hapmap]
rs17385407	0.86[CEU][hapmap]
rs1809963	0.86[CEU][hapmap]
rs1998651	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2025516	0.91[CEU][hapmap];0.80[ASN][1000 genomes]
rs2025517	0.86[CEU][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2083128	0.86[CEU][hapmap]
rs2753260	0.86[CEU][hapmap]
rs3733264	0.86[CEU][hapmap]
rs3733265	0.86[CEU][hapmap]
rs3733266	0.86[CEU][hapmap]
rs3766385	0.82[CEU][hapmap]
rs3766387	0.91[CEU][hapmap]
rs3766388	0.86[CEU][hapmap]
rs3766389	0.86[CEU][hapmap]
rs3816146	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4106115	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5002947	0.91[CEU][hapmap]
rs6427535	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6656191	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660233	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6668760	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6670721	0.91[CEU][hapmap]
rs6687641	0.86[CEU][hapmap]
rs6692382	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7515302	0.91[ASN][1000 genomes]
rs7528976	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534679	0.85[EUR][1000 genomes]
rs7547054	0.86[CEU][hapmap]
rs7550771	0.86[CEU][hapmap]
rs912582	0.82[CEU][hapmap]
rs9726326	0.85[EUR][1000 genomes]
rs977019	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2099604	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160505000-160505800	ZNF genes & repeats	Dnd41	blood
2	chr1:160505400-160508400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160505600-160506200	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links