Variant report

Variant	rs10877040
Chromosome Location	chr12:58326448-58326449
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	chr12:58322404..58324833-chr12:58326423..58328492,2	MCF-7	breast:
5	chr12:58153870..58155501-chr12:58325931..58327914,2	K562	blood:

Variant related genes	Relation type
ENSG00000257698	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10431506	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783857	0.87[AMR][1000 genomes]
rs10783858	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877039	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877041	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172387	0.81[EUR][1000 genomes]
rs11172388	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172389	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2372309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751325	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751326	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751327	0.91[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4630335	1.00[YRI][hapmap]
rs4760174	0.81[EUR][1000 genomes]
rs4760344	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760346	0.80[EUR][1000 genomes]
rs6581159	0.83[CEU][hapmap]
rs7136981	0.81[EUR][1000 genomes]
rs7298370	0.81[EUR][1000 genomes]
rs7358584	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9971803	0.96[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10877040	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877040	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877040	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10877040	XRCC6BP1	cis	lesional skin	skin_eQTL
rs10877040	KUB3	cis	multi-tissue	Pritchard
rs10877040	XRCC6BP1	cis	Whole Blood	GTEx
rs10877040	XRCC6BP1	cis	normal skin	skin_eQTL
rs10877040	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877040	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10877040	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs10877040	XRCC6BP1	cis	multi-tissue	Pritchard
rs10877040	XRCC6BP1	cis	Stomach	GTEx
rs10877040	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877040	XRCC6BP1	cis	Artery Aorta	GTEx
rs10877040	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877040	XRCC6BP1	cis	Thyroid	GTEx
rs10877040	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10877040	XRCC6BP1	cis	lung	GTEx
rs10877040	XRCC6BP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:32 , 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
32	chr12:58326400-58328400	Weak transcription	Fetal Heart	heart

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