Variant report

Variant	rs12308413
Chromosome Location	chr12:58326219-58326220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58319307..58323432-chr12:58323969..58328289,4	K562	blood:
2	chr12:58325555..58327910-chr12:58329455..58331611,2	K562	blood:
3	chr12:58325963..58328305-chr12:58337934..58340294,2	K562	blood:
4	chr12:58153870..58155501-chr12:58325931..58327914,2	K562	blood:

Variant related genes	Relation type
ENSG00000257698	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10122	0.97[EUR][1000 genomes]
rs10783859	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877036	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877037	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172387	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2888288	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4272820	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4335583	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4373979	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4509811	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4534624	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4583019	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760174	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760343	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760346	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760347	0.97[EUR][1000 genomes]
rs6581159	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133278	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7136981	0.96[EUR][1000 genomes]
rs7295748	0.98[EUR][1000 genomes]
rs7298370	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7299249	0.97[EUR][1000 genomes]
rs7975227	0.90[EUR][1000 genomes]
rs7978588	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9971722	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12308413	XRCC6BP1	cis	lung	GTEx
rs12308413	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs12308413	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs12308413	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12308413	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs12308413	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12308413	XRCC6BP1	cis	Thyroid	GTEx
rs12308413	XRCC6BP1	cis	Whole Blood	GTEx
rs12308413	XRCC6BP1	cis	Nerve Tibial	GTEx
rs12308413	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs12308413	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs12308413	XRCC6BP1	cis	Artery Tibial	GTEx
rs12308413	XRCC6BP1	cis	Artery Aorta	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58317400-58328600	Weak transcription	Psoas Muscle	Psoas
2	chr12:58321200-58328000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:58321400-58329600	Weak transcription	Ovary	ovary
4	chr12:58323000-58328600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:58323200-58329200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:58323600-58327600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:58323600-58328600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:58323800-58328200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:58323800-58329000	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:58323800-58329000	Weak transcription	HUVEC	blood vessel
11	chr12:58324200-58327200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:58324200-58329400	Weak transcription	Fetal Stomach	stomach
13	chr12:58324400-58328600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:58324400-58328600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:58324400-58328800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:58324800-58329200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:58325000-58329200	Weak transcription	Adipose Nuclei	Adipose
18	chr12:58325200-58326600	Weak transcription	Dnd41	blood
19	chr12:58325200-58327800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:58325200-58328200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:58325200-58328800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:58325200-58329000	Weak transcription	HSMMtube	muscle
23	chr12:58325400-58328200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:58325600-58329200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:58326000-58328600	Weak transcription	Brain Anterior Caudate	brain
26	chr12:58326200-58327200	Weak transcription	Fetal Thymus	thymus
27	chr12:58326200-58327400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:58326200-58327600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:58326200-58327600	Weak transcription	Thymus	Thymus
30	chr12:58326200-58328800	Weak transcription	Osteobl	bone
31	chr12:58326200-58329000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links