Variant report

Variant	rs10877041
Chromosome Location	chr12:58328500-58328501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58327474..58329106-chr12:58333139..58335115,2	MCF-7	breast:
2	chr12:58328024..58328544-chr8:128241140..128241739,2	Hela-S3	cervix:
3	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
4	chr12:58321883..58323432-chr12:58326789..58329565,2	K562	blood:
5	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
6	chr12:57915577..57917168-chr12:58328157..58330221,2	K562	blood:
7	chr12:58306776..58308990-chr12:58327351..58329444,2	K562	blood:
8	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000123427	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257921	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10431506	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747788	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783857	0.85[AMR][1000 genomes]
rs10783858	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877039	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877040	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172387	0.81[EUR][1000 genomes]
rs11172388	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2372309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751326	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751327	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4373979	0.81[EUR][1000 genomes]
rs4509811	0.81[EUR][1000 genomes]
rs4534624	0.81[EUR][1000 genomes]
rs4590915	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760174	0.81[EUR][1000 genomes]
rs4760344	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760346	0.80[EUR][1000 genomes]
rs7136981	0.81[EUR][1000 genomes]
rs7298370	0.81[EUR][1000 genomes]
rs7358584	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9971803	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs10877041	XRCC6BP1	cis	Artery Aorta	GTEx
rs10877041	KUB3	cis	multi-tissue	Pritchard
rs10877041	XRCC6BP1	cis	Lymphoblastoid	GTEx
rs10877041	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877041	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs10877041	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10877041	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877041	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877041	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10877041	XRCC6BP1	cis	Thyroid	GTEx
rs10877041	XRCC6BP1	cis	multi-tissue	Pritchard
rs10877041	KIAA0748	cis	cerebellum	SCAN
rs10877041	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877041	XRCC6BP1	cis	normal skin	skin_eQTL
rs10877041	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877041	FAM119B	cis	cerebellum	SCAN
rs10877041	XRCC6BP1	cis	lung	GTEx
rs10877041	XRCC6BP1	cis	Stomach	GTEx
rs10877041	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs10877041	XRCC6BP1	cis	parietal	SCAN
rs10877041	XRCC6BP1	cis	Whole Blood	GTEx
rs10877041	XRCC6BP1	cis	lesional skin	skin_eQTL
rs10877041	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10877041	XRCC6BP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58317400-58328600	Weak transcription	Psoas Muscle	Psoas
2	chr12:58321400-58329600	Weak transcription	Ovary	ovary
3	chr12:58323000-58328600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:58323200-58329200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:58323600-58328600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:58323800-58329000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:58323800-58329000	Weak transcription	HUVEC	blood vessel
8	chr12:58324200-58329400	Weak transcription	Fetal Stomach	stomach
9	chr12:58324400-58328600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:58324400-58328600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:58324400-58328800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:58324800-58329200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:58325000-58329200	Weak transcription	Adipose Nuclei	Adipose
14	chr12:58325200-58328800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:58325200-58329000	Weak transcription	HSMMtube	muscle
16	chr12:58325600-58329200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:58326000-58328600	Weak transcription	Brain Anterior Caudate	brain
18	chr12:58326200-58328800	Weak transcription	Osteobl	bone
19	chr12:58326200-58329000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:58327000-58329600	Weak transcription	Left Ventricle	heart
21	chr12:58327600-58330000	Active TSS	Fetal Thymus	thymus
22	chr12:58327600-58330400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:58327600-58330400	Active TSS	Thymus	Thymus
24	chr12:58327800-58328800	Weak transcription	Brain Angular Gyrus	brain
25	chr12:58327800-58328800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr12:58327800-58329200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:58327800-58329400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:58327800-58329400	Flanking Active TSS	Dnd41	blood
29	chr12:58327800-58329600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:58328000-58329000	Enhancers	Fetal Brain Female	brain
31	chr12:58328000-58329400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr12:58328000-58329800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:58328200-58328600	Weak transcription	Brain Germinal Matrix	brain
34	chr12:58328200-58328600	Active TSS	K562	blood
35	chr12:58328200-58328800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:58328200-58328800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:58328200-58329000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:58328200-58329200	Enhancers	Primary B cells from cord blood	blood
39	chr12:58328200-58329200	Enhancers	Colon Smooth Muscle	Colon
40	chr12:58328400-58328600	Enhancers	GM12878-XiMat	blood
41	chr12:58328400-58328600	Enhancers	NHDF-Ad	bronchial
42	chr12:58328400-58329000	Enhancers	Fetal Heart	heart
43	chr12:58328400-58329000	Enhancers	Stomach Smooth Muscle	stomach
44	chr12:58328400-58329200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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