Variant report

Variant	rs4604932
Chromosome Location	chr12:58353258-58353259
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	chr12:58339593..58341366-chr12:58350590..58353556,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506393	0.84[EUR][1000 genomes]
rs10783860	0.80[EUR][1000 genomes]
rs10783865	0.82[EUR][1000 genomes]
rs10877048	0.89[EUR][1000 genomes]
rs10877052	0.83[EUR][1000 genomes]
rs11172408	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172418	0.84[EUR][1000 genomes]
rs11172420	0.84[EUR][1000 genomes]
rs11172421	0.83[EUR][1000 genomes]
rs11172422	0.83[EUR][1000 genomes]
rs11608333	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12366757	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12366794	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12368024	0.83[EUR][1000 genomes]
rs12422985	0.83[EUR][1000 genomes]
rs12825843	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12828647	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1466973	0.84[EUR][1000 genomes]
rs1605333	0.84[EUR][1000 genomes]
rs2221541	0.83[EUR][1000 genomes]
rs2372378	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2372379	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3858557	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3858558	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3933982	0.90[EUR][1000 genomes]
rs4495927	0.84[EUR][1000 genomes]
rs4565944	0.81[EUR][1000 genomes]
rs4760175	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4760181	0.82[EUR][1000 genomes]
rs4760182	0.83[EUR][1000 genomes]
rs6581170	0.82[EUR][1000 genomes]
rs6581173	0.82[EUR][1000 genomes]
rs6581177	0.81[EUR][1000 genomes]
rs7132168	0.81[EUR][1000 genomes]
rs7132521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7135063	0.82[EUR][1000 genomes]
rs7304458	0.83[EUR][1000 genomes]
rs7314066	0.81[EUR][1000 genomes]
rs7484670	0.84[EUR][1000 genomes]
rs7954291	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7959747	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7960690	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7960942	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7963367	0.83[EUR][1000 genomes]
rs7974754	0.84[EUR][1000 genomes]
rs7975805	0.84[EUR][1000 genomes]
rs7977671	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs871908	0.82[EUR][1000 genomes]
rs951901	0.83[EUR][1000 genomes]
rs970249	0.82[EUR][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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases
2	nsv523853	chr12:58350631-58386722	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv975500	chr12:58351052-58362673	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4604932	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4604932	XRCC6BP1	cis	Artery Aorta	GTEx
rs4604932	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4604932	XRCC6BP1	cis	Artery Tibial	GTEx
rs4604932	XRCC6BP1	cis	Whole Blood	GTEx
rs4604932	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs4604932	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4604932	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4604932	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4604932	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4604932	XRCC6BP1	cis	lung	GTEx
rs4604932	XRCC6BP1	cis	Thyroid	GTEx
rs4604932	XRCC6BP1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58336200-58353400	Weak transcription	Fetal Kidney	kidney
2	chr12:58336200-58353600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:58336200-58353600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:58336200-58353800	Weak transcription	Brain Angular Gyrus	brain
5	chr12:58336200-58353800	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:58336200-58354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:58336200-58354000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:58336200-58354000	Weak transcription	Psoas Muscle	Psoas
9	chr12:58336200-58356200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:58336200-58359600	Weak transcription	A549	lung
11	chr12:58336400-58359600	Weak transcription	HMEC	breast
12	chr12:58337200-58358400	Weak transcription	HepG2	liver
13	chr12:58348800-58353800	Weak transcription	Osteobl	bone
14	chr12:58350600-58355400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:58351200-58359400	Weak transcription	K562	blood
16	chr12:58351400-58355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:58351800-58353600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:58351800-58354400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:58352000-58353400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:58352200-58353600	Weak transcription	Brain Anterior Caudate	brain
21	chr12:58352200-58354800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:58352200-58358200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:58352400-58353400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:58352400-58353600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:58352400-58353800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:58352400-58354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:58352400-58354000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:58352400-58354000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:58352400-58354200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:58352400-58354200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:58352400-58354400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:58352400-58354600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:58352400-58354600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:58352400-58354600	Weak transcription	Left Ventricle	heart
35	chr12:58352400-58355600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:58352400-58359400	Weak transcription	Placenta	Placenta
37	chr12:58352600-58353600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:58352600-58353600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:58352600-58353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:58352600-58353600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:58352600-58353600	Weak transcription	Colonic Mucosa	Colon
42	chr12:58352600-58354000	Weak transcription	Adipose Nuclei	Adipose
43	chr12:58352600-58354200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:58352600-58354200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:58352600-58354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:58352600-58354600	Weak transcription	Fetal Lung	lung
47	chr12:58352600-58354600	Weak transcription	Right Ventricle	heart
48	chr12:58352600-58354800	Weak transcription	Primary B cells from cord blood	blood
49	chr12:58352600-58355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:58352600-58357800	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links