Variant report

Variant	rs12065420
Chromosome Location	chr1:160812311-160812312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160805876..160809429-chr1:160811999..160815816,3	K562	blood:
2	chr1:160805876..160808335-chr1:160811999..160814822,2	K562	blood:
3	chr1:160811365..160813058-chr1:160817059..160818706,2	K562	blood:

Variant related genes	Relation type
ENSG00000226003	Chromatin interaction
ENSG00000122223	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11265494	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11265495	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11265508	1.00[MEX][hapmap]
rs12059277	1.00[MEX][hapmap]
rs12060017	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073515	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074019	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084061	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs12090411	1.00[MEX][hapmap]
rs12094026	1.00[MEX][hapmap]
rs12095453	1.00[MEX][hapmap]
rs12095682	1.00[MEX][hapmap]
rs12354107	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12354108	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832317	1.00[MEX][hapmap]
rs16832484	1.00[MEX][hapmap]
rs16832486	0.87[AMR][1000 genomes]
rs16832506	1.00[AMR][1000 genomes]
rs35918317	1.00[MEX][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12065420	CT47A3	trans	lymphoblastoid	seeQTL
rs12065420	CT47A5	trans	lymphoblastoid	seeQTL
rs12065420	CT47A11	trans	lymphoblastoid	seeQTL
rs12065420	CT47A8	trans	lymphoblastoid	seeQTL
rs12065420	CT47A9	trans	lymphoblastoid	seeQTL
rs12065420	CT47A1	trans	lymphoblastoid	seeQTL
rs12065420	CT47A2	trans	lymphoblastoid	seeQTL
rs12065420	CT47A10	trans	lymphoblastoid	seeQTL
rs12065420	CT47A4	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 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	chr1:160808600-160812600	Genic enhancers	Primary hematopoietic stem cells	blood
3	chr1:160808800-160812600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:160809000-160812400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:160809000-160812800	Enhancers	Thymus	Thymus
6	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:160809000-160814200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:160809000-160814400	Weak transcription	Spleen	Spleen
10	chr1:160809200-160812600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:160809200-160814400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:160809200-160814800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:160810200-160814800	Weak transcription	Dnd41	blood
14	chr1:160810200-160815000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:160810600-160813000	Enhancers	Fetal Thymus	thymus
16	chr1:160810600-160814400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:160811400-160820200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:160811600-160812400	Enhancers	Left Ventricle	heart
19	chr1:160811600-160813000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:160811800-160814200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:160811800-160814400	Weak transcription	Fetal Intestine Large	intestine
22	chr1:160811800-160815000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:160811800-160824600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:160812000-160812600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:160812000-160813000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:160812200-160812600	Enhancers	Fetal Heart	heart
27	chr1:160812200-160814400	Weak transcription	Primary T cells fromperipheralblood	blood

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