Variant report

Variant	rs10908796
Chromosome Location	chr1:160575373-160575374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1061217	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10752638	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797083	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908789	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908792	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908794	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265442	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265443	0.81[ASN][1000 genomes]
rs11265444	0.91[ASN][1000 genomes]
rs11265449	0.92[ASN][1000 genomes]
rs11265451	0.89[ASN][1000 genomes]
rs1138323	0.85[EUR][1000 genomes]
rs12048466	0.89[ASN][1000 genomes]
rs12144628	0.83[EUR][1000 genomes]
rs12402879	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12728784	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12736781	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394079	0.98[ASN][1000 genomes]
rs1572382	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1604783	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1998651	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2089088	0.89[ASN][1000 genomes]
rs2099604	0.83[EUR][1000 genomes]
rs2102225	0.89[ASN][1000 genomes]
rs2102226	0.89[ASN][1000 genomes]
rs2369725	0.89[ASN][1000 genomes]
rs2369726	0.89[ASN][1000 genomes]
rs3816146	0.83[EUR][1000 genomes]
rs6427535	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668760	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692382	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526815	0.96[ASN][1000 genomes]
rs7534679	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs927202	0.89[ASN][1000 genomes]
rs977019	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10908796	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160558000-160575400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:160574000-160578800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:160574200-160576200	Weak transcription	Thymus	Thymus
4	chr1:160574800-160575600	Enhancers	GM12878-XiMat	blood
5	chr1:160575000-160575800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:160575000-160577400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr1:160575000-160577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:160575200-160575600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:160575200-160576400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:160575200-160577200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:160575200-160577400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:160575200-160577600	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:160575200-160577600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:160575200-160577600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:160575200-160577800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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