Variant report

Variant	rs578608
Chromosome Location	chr1:160819717-160819718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11265493	0.82[AMR][1000 genomes]
rs11265496	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11582719	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11587898	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319651	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280415	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2779790	0.93[EUR][1000 genomes]
rs2779792	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2990702	0.93[EUR][1000 genomes]
rs2990703	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753389	0.90[EUR][1000 genomes]
rs3766379	0.91[EUR][1000 genomes]
rs4656937	0.89[EUR][1000 genomes]
rs4656938	0.91[EUR][1000 genomes]
rs483197	0.93[EUR][1000 genomes]
rs489651	0.94[EUR][1000 genomes]
rs491061	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499721	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs512525	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535610	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536906	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537957	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541834	0.93[EUR][1000 genomes]
rs549565	0.93[EUR][1000 genomes]
rs60755678	0.87[EUR][1000 genomes]
rs6671710	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682654	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518342	0.84[AMR][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	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	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv946456	chr1:160812650-160824679	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs578608	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160811400-160820200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:160811800-160824600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:160812800-160824200	Weak transcription	Thymus	Thymus
4	chr1:160814800-160820200	Weak transcription	Fetal Intestine Large	intestine
5	chr1:160815400-160820600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:160816800-160820200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:160817800-160821200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:160817800-160825400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:160819000-160820200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:160819200-160821200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:160819200-160823200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:160819400-160820600	Weak transcription	Spleen	Spleen
13	chr1:160819400-160822400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:160819600-160820800	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links