Variant report

Variant	rs2779790
Chromosome Location	chr1:160815360-160815361
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	TEAD4	chr1:160815052-160815455	K562	blood:	n/a	n/a
2	GATA1	chr1:160815045-160815579	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160805876..160809429-chr1:160811999..160815816,3	K562	blood:
2	chr1:160815023..160816835-chr1:160823211..160824951,2	K562	blood:

Variant related genes	Relation type
ENSG00000226003	TF binding region
ENSG00000122223	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11265493	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11265496	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11582719	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11587898	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1319651	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2139660	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2280415	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779792	0.97[EUR][1000 genomes]
rs2990702	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2990703	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3753389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766379	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656936	0.90[ASN][1000 genomes]
rs4656937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656938	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483197	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs489651	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491061	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs499721	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512525	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs535610	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs536906	0.98[EUR][1000 genomes]
rs537957	0.97[EUR][1000 genomes]
rs541834	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578608	0.93[EUR][1000 genomes]
rs60755678	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671710	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6682654	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7518342	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[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	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
rs2779790	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 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	chr1:160812400-160816600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:160812600-160816000	Weak transcription	Fetal Heart	heart
5	chr1:160812600-160816800	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:160812800-160816800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:160812800-160824200	Weak transcription	Thymus	Thymus
8	chr1:160813400-160815400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:160814200-160815400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:160814400-160815400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:160814400-160815400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:160814800-160820200	Weak transcription	Fetal Intestine Large	intestine
13	chr1:160815000-160815400	Enhancers	Primary T cells from cord blood	blood
14	chr1:160815000-160815400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:160815000-160816200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:160815000-160817800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:160815200-160815800	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links