Variant report

Variant	rs10444569
Chromosome Location	chr12:58269529-58269530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58240648..58242325-chr12:58268163..58269824,2	MCF-7	breast:
2	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
3	chr12:58263220..58265697-chr12:58267333..58269634,2	MCF-7	breast:
4	chr12:58262380..58265069-chr12:58266414..58270393,4	K562	blood:
5	chr12:58269021..58271713-chr12:58278735..58281292,2	MCF-7	breast:
6	chr12:58242941..58244963-chr12:58268081..58270017,2	MCF-7	breast:
7	chr12:58268216..58270366-chr12:58282645..58284163,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10747784	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747786	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747787	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783850	0.87[AMR][1000 genomes]
rs10783851	0.87[AMR][1000 genomes]
rs10783854	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783855	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10783856	0.89[AMR][1000 genomes];0.84[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];0.94[ASN][1000 genomes]
rs10877030	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877031	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877032	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172362	0.83[AMR][1000 genomes]
rs11172367	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172368	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172369	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172375	0.82[ASN][1000 genomes]
rs11172378	0.82[ASN][1000 genomes]
rs12312955	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12319233	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426201	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1599750	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599751	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599931	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875125	0.86[AMR][1000 genomes]
rs1962047	0.83[ASN][1000 genomes]
rs2002275	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs4237844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760172	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760332	0.82[AMR][1000 genomes]
rs4760335	0.81[AMR][1000 genomes]
rs4760339	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760340	0.80[ASN][1000 genomes]
rs4760341	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5017863	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59401446	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581157	0.84[ASN][1000 genomes]
rs7134797	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312623	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489290	0.81[AMR][1000 genomes]
rs7969844	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870392	0.82[AMR][1000 genomes]
rs9645819	0.88[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10444569	XRCC6BP1	cis	Whole Blood	GTEx
rs10444569	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10444569	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10444569	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10444569	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10444569	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10444569	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10444569	METTL21B	cis	lung	GTEx
rs10444569	XRCC6BP1	cis	lung	GTEx
rs10444569	XRCC6BP1	cis	Artery Tibial	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
2	chr12:58262400-58269600	Weak transcription	Fetal Heart	heart
3	chr12:58263000-58269800	Weak transcription	Lung	lung
4	chr12:58263200-58271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:58263600-58269600	Weak transcription	NHLF	lung
6	chr12:58263600-58275000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:58263800-58269600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:58264000-58269600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:58264400-58269600	Weak transcription	Brain Substantia Nigra	brain
10	chr12:58264400-58269600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:58264400-58269800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:58267600-58270000	Enhancers	K562	blood
13	chr12:58268400-58275000	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:58268600-58269600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:58268600-58269800	Weak transcription	Fetal Lung	lung
16	chr12:58268800-58269600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:58268800-58269800	Weak transcription	Brain Angular Gyrus	brain
18	chr12:58268800-58269800	Weak transcription	Left Ventricle	heart
19	chr12:58268800-58269800	Weak transcription	Right Ventricle	heart
20	chr12:58268800-58270000	Weak transcription	Colonic Mucosa	Colon
21	chr12:58268800-58270000	Weak transcription	Placenta	Placenta
22	chr12:58268800-58270000	Weak transcription	Fetal Stomach	stomach
23	chr12:58268800-58270200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:58268800-58270600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr12:58268800-58275200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:58268800-58275600	Weak transcription	Stomach Mucosa	stomach
27	chr12:58269200-58269600	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:58269200-58269600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:58269400-58269600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:58269400-58269600	Enhancers	Osteobl	bone
31	chr12:58269400-58270000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:58269400-58270200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:58269400-58270200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:58269400-58270200	Enhancers	GM12878-XiMat	blood
35	chr12:58269400-58270400	Enhancers	Psoas Muscle	Psoas
36	chr12:58269400-58270400	Enhancers	Right Atrium	heart
37	chr12:58269400-58270600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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