Variant report

Variant	rs59401446
Chromosome Location	chr12:58259564-58259565
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58257328..58259688-chr12:58290813..58293614,3	MCF-7	breast:
2	chr12:58259030..58259709-chr6:12008751..12009401,2	Hela-S3	cervix:
3	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
4	chr12:58256926..58259595-chr12:58266193..58268490,2	K562	blood:
5	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
6	chr12:58234242..58236619-chr12:58259394..58262193,2	MCF-7	breast:
7	chr12:58251247..58254157-chr12:58257386..58260333,2	K562	blood:
8	chr12:58259134..58259709-chr14:60558115..60559114,2	Hela-S3	cervix:
9	chr12:58206839..58209461-chr12:58258258..58260361,2	MCF-7	breast:
10	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:
11	chr12:58259261..58259822-chr7:148638155..148639112,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000258553	Chromatin interaction
ENSG00000095951	Chromatin interaction
ENSG00000126773	Chromatin interaction
ENSG00000252310	Chromatin interaction
ENSG00000269903	Chromatin interaction
ENSG00000135407	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10444569	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747784	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747786	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747787	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783854	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783855	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10783856	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10877029	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877030	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877031	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877032	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172361	0.82[AMR][1000 genomes]
rs11172367	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172368	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172369	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12312955	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12319233	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12426201	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599750	0.87[AMR][1000 genomes]
rs1599751	0.87[AMR][1000 genomes]
rs1599931	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1962047	0.80[ASN][1000 genomes]
rs2002275	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3751331	0.80[ASN][1000 genomes]
rs4237844	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760172	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760335	0.81[AMR][1000 genomes]
rs4760339	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760340	0.80[ASN][1000 genomes]
rs4760341	0.93[ASN][1000 genomes]
rs5017863	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581157	0.81[ASN][1000 genomes]
rs7134797	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312623	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7489290	0.81[AMR][1000 genomes]
rs7969844	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9645819	0.99[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs59401446	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs59401446	XRCC6BP1	cis	Artery Aorta	GTEx
rs59401446	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs59401446	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs59401446	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs59401446	XRCC6BP1	cis	Artery Tibial	GTEx
rs59401446	METTL21B	cis	lung	GTEx
rs59401446	XRCC6BP1	cis	lung	GTEx
rs59401446	XRCC6BP1	cis	Whole Blood	GTEx
rs59401446	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs59401446	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs59401446	METTL21B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

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	chr12:58257600-58259600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:58258400-58259600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr12:58258400-58259600	Active TSS	Fetal Brain Female	brain
6	chr12:58258400-58259800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr12:58258600-58259600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:58258600-58259600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:58258600-58259600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:58258600-58259600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:58258600-58259600	Active TSS	Fetal Kidney	kidney
12	chr12:58258600-58259600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:58258600-58259600	Active TSS	Ovary	ovary
14	chr12:58258600-58259600	Active TSS	Right Atrium	heart
15	chr12:58258600-58259600	Active TSS	Right Ventricle	heart
16	chr12:58258600-58259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:58258600-58259800	Active TSS	Brain Hippocampus Middle	brain
18	chr12:58258600-58259800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:58258600-58261800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:58258600-58262000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:58258600-58262200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:58258800-58259600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:58258800-58259600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:58258800-58259600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:58258800-58259600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:58258800-58259600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:58258800-58259600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:58258800-58259600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:58258800-58259600	Active TSS	Brain Substantia Nigra	brain
30	chr12:58258800-58259600	Active TSS	Colonic Mucosa	Colon
31	chr12:58258800-58259600	Active TSS	Colon Smooth Muscle	Colon
32	chr12:58258800-58259600	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:58258800-58259600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:58258800-58259600	Active TSS	Left Ventricle	heart
35	chr12:58258800-58259600	Active TSS	Psoas Muscle	Psoas
36	chr12:58258800-58259600	Active TSS	A549	lung
37	chr12:58258800-58259600	Bivalent Enhancer	Dnd41	blood
38	chr12:58258800-58259600	Flanking Active TSS	GM12878-XiMat	blood
39	chr12:58258800-58259600	Flanking Active TSS	HMEC	breast
40	chr12:58258800-58259800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr12:58258800-58259800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:58258800-58259800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:58259000-58259600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr12:58259000-58259600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:58259000-58259600	Active TSS	Lung	lung
46	chr12:58259000-58259600	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr12:58259000-58259600	Active TSS	Small Intestine	intestine
48	chr12:58259000-58259600	Active TSS	HSMM	muscle
49	chr12:58259000-58259800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr12:58259000-58259800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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