Variant report

Variant	rs4760333
Chromosome Location	chr12:58224040-58224041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58217743..58220104-chr12:58222008..58224494,2	MCF-7	breast:
2	chr12:58218535..58220523-chr12:58222880..58224447,2	K562	blood:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000207789	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10747784	0.80[EUR][1000 genomes]
rs10783850	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783851	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783854	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783855	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783856	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877022	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877024	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877025	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877026	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10877029	0.83[AMR][1000 genomes]
rs10877030	0.83[AMR][1000 genomes]
rs11172361	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172362	0.81[EUR][1000 genomes]
rs1599750	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599751	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1875125	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760171	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760172	0.83[AMR][1000 genomes]
rs4760332	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760335	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7489290	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7965287	0.82[AFR][1000 genomes]
rs870392	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871871	0.94[AMR][1000 genomes];1.00[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
rs4760333	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760333	METTL21B	cis	Whole Blood	GTEx
rs4760333	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760333	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760333	METTL21B	cis	Muscle Skeletal	GTEx
rs4760333	METTL21B	cis	Esophagus Muscularis	GTEx
rs4760333	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760333	XRCC6BP1	cis	Whole Blood	GTEx
rs4760333	XRCC6BP1	cis	lung	GTEx
rs4760333	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4760333	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs4760333	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58211400-58224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:58211400-58224800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58212000-58224400	Strong transcription	Fetal Intestine Large	intestine
5	chr12:58212000-58224800	Strong transcription	Thymus	Thymus
6	chr12:58212200-58224800	Strong transcription	Brain Germinal Matrix	brain
7	chr12:58212600-58224200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:58213600-58224400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:58215400-58227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:58217200-58224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:58217400-58225400	Strong transcription	HepG2	liver
12	chr12:58220600-58225600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:58221000-58224600	Strong transcription	K562	blood
14	chr12:58221400-58224800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:58222400-58224400	Genic enhancers	Brain Anterior Caudate	brain
16	chr12:58222400-58224600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
17	chr12:58222600-58225400	Weak transcription	NHEK	skin
18	chr12:58222800-58224400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:58222800-58224600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:58222800-58224800	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr12:58222800-58224800	Genic enhancers	Lung	lung
22	chr12:58222800-58225400	Weak transcription	HSMMtube	muscle
23	chr12:58222800-58230200	Enhancers	Right Atrium	heart
24	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
25	chr12:58223000-58224400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:58223000-58224400	Weak transcription	Stomach Mucosa	stomach
27	chr12:58223000-58224400	Genic enhancers	Spleen	Spleen
28	chr12:58223000-58224600	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr12:58223000-58225000	Weak transcription	Small Intestine	intestine
30	chr12:58223000-58225200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:58223000-58225400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:58223000-58225400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:58223000-58228400	Genic enhancers	Fetal Thymus	thymus
34	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr12:58223200-58224400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:58223200-58225200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr12:58223200-58225400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:58223200-58225400	Weak transcription	HMEC	breast
39	chr12:58223400-58224200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:58223400-58224400	Weak transcription	Fetal Brain Male	brain
41	chr12:58223400-58225000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:58223400-58225000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:58223400-58225000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:58223400-58225000	Weak transcription	Fetal Brain Female	brain
45	chr12:58223400-58225000	Weak transcription	NHDF-Ad	bronchial
46	chr12:58223400-58225200	Weak transcription	A549	lung
47	chr12:58223400-58225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:58223400-58225400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:58223400-58225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:58223400-58225400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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