Variant report

Variant	rs2990703
Chromosome Location	chr1:160811830-160811831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160720732..160722587-chr1:160809717..160812109,2	K562	blood:
2	chr1:160811365..160813058-chr1:160817059..160818706,2	K562	blood:

Variant related genes	Relation type
ENSG00000226003	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11265493	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs11265496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11582719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11587898	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2139660	0.84[CEU][hapmap]
rs2280415	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2779790	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2779792	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2990702	0.98[EUR][1000 genomes]
rs3753389	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766379	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656937	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4656938	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs483197	0.97[EUR][1000 genomes]
rs489651	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs491061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499721	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs512525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536906	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541834	0.98[EUR][1000 genomes]
rs549565	0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[EUR][1000 genomes]
rs578608	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60755678	0.92[EUR][1000 genomes]
rs6671710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518342	0.84[CEU][hapmap];0.83[AMR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2990703	CD244	cis	multi-tissue	Pritchard
rs2990703	CD244	cis	Lymphoblastoid	GTEx
rs2990703	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160803200-160812400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:160808200-160812200	Weak transcription	Fetal Heart	heart
3	chr1:160808600-160812600	Genic enhancers	Primary hematopoietic stem cells	blood
4	chr1:160808800-160812600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:160809000-160812400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:160809000-160812800	Enhancers	Thymus	Thymus
7	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:160809000-160814200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:160809000-160814400	Weak transcription	Spleen	Spleen
11	chr1:160809200-160812600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:160809200-160814400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:160809200-160814800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:160810200-160814800	Weak transcription	Dnd41	blood
15	chr1:160810200-160815000	Weak transcription	Primary T cells from cord blood	blood
16	chr1:160810400-160812000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:160810600-160813000	Enhancers	Fetal Thymus	thymus
18	chr1:160810600-160814400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:160811200-160812200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:160811400-160820200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:160811600-160812000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:160811600-160812200	Enhancers	Gastric	stomach
23	chr1:160811600-160812400	Enhancers	Left Ventricle	heart
24	chr1:160811600-160813000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:160811800-160814200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:160811800-160814400	Weak transcription	Fetal Intestine Large	intestine
27	chr1:160811800-160815000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:160811800-160824600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links