Variant report

Variant	rs12426201
Chromosome Location	chr12:58259752-58259753
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
2	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
3	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
4	chr12:58234242..58236619-chr12:58259394..58262193,2	MCF-7	breast:
5	chr12:58251247..58254157-chr12:58257386..58260333,2	K562	blood:
6	chr12:58206839..58209461-chr12:58258258..58260361,2	MCF-7	breast:
7	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:
8	chr12:58259698..58262580-chr5:154319260..154321205,2	MCF-7	breast:
9	chr12:58259261..58259822-chr7:148638155..148639112,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000269903	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000252310	Chromatin interaction
ENSG00000082515	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10444569	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747784	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747786	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747787	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783850	0.87[AMR][1000 genomes]
rs10783851	0.87[AMR][1000 genomes]
rs10783854	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10783855	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783856	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10877024	0.87[AMR][1000 genomes]
rs10877025	0.87[AMR][1000 genomes]
rs10877026	0.86[AMR][1000 genomes]
rs10877029	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877030	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172362	0.83[AMR][1000 genomes]
rs11172367	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172368	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172369	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172371	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172375	0.81[ASN][1000 genomes]
rs11172378	0.81[ASN][1000 genomes]
rs12312955	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12319233	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1599750	0.89[AMR][1000 genomes]
rs1599751	0.89[AMR][1000 genomes]
rs1599931	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875125	0.86[AMR][1000 genomes]
rs1962047	0.83[ASN][1000 genomes]
rs2002275	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs4237844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760172	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760332	0.82[AMR][1000 genomes]
rs4760335	0.81[AMR][1000 genomes]
rs4760339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760341	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5017863	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59401446	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581157	0.83[ASN][1000 genomes]
rs7134797	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312623	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489290	0.81[AMR][1000 genomes]
rs7969844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870392	0.82[AMR][1000 genomes]
rs9645819	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12426201	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs12426201	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs12426201	XRCC6BP1	cis	Whole Blood	GTEx
rs12426201	XRCC6BP1	cis	Artery Tibial	GTEx
rs12426201	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs12426201	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12426201	METTL21B	cis	lung	GTEx
rs12426201	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs12426201	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
2	chr12:58257000-58260000	Enhancers	Fetal Brain Male	brain
3	chr12:58258400-58259800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr12:58258600-58259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:58258600-58259800	Active TSS	Brain Hippocampus Middle	brain
6	chr12:58258600-58259800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:58258600-58261800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:58258600-58262000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:58258600-58262200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:58258800-58259800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:58258800-58259800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:58258800-58259800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:58259000-58259800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:58259000-58259800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:58259000-58259800	Enhancers	Fetal Heart	heart
16	chr12:58259200-58259800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:58259200-58259800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:58259200-58259800	Enhancers	Stomach Mucosa	stomach
19	chr12:58259200-58260000	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr12:58259400-58259800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr12:58259400-58259800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:58259400-58259800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:58259400-58259800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:58259400-58259800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:58259400-58259800	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr12:58259400-58259800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr12:58259400-58259800	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr12:58259400-58259800	Flanking Active TSS	Fetal Lung	lung
29	chr12:58259400-58259800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr12:58259400-58259800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:58259400-58259800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:58259400-58259800	Flanking Active TSS	Hela-S3	cervix
33	chr12:58259400-58259800	Flanking Active TSS	HUVEC	blood vessel
34	chr12:58259400-58259800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:58259400-58259800	Flanking Active TSS	NHDF-Ad	bronchial
36	chr12:58259400-58259800	Flanking Active TSS	NHEK	skin
37	chr12:58259400-58259800	Flanking Active TSS	Osteobl	bone
38	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
39	chr12:58259600-58259800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr12:58259600-58259800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr12:58259600-58259800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:58259600-58259800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:58259600-58259800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr12:58259600-58259800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
45	chr12:58259600-58259800	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:58259600-58259800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr12:58259600-58259800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:58259600-58259800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:58259600-58259800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:58259600-58259800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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