Variant report

Variant	rs4760339
Chromosome Location	chr12:58268149-58268150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
2	chr12:58263220..58265697-chr12:58267333..58269634,2	MCF-7	breast:
3	chr12:58256926..58259595-chr12:58266193..58268490,2	K562	blood:
4	chr12:58262380..58265069-chr12:58266414..58270393,4	K562	blood:
5	chr12:58242941..58244963-chr12:58268081..58270017,2	MCF-7	breast:
6	chr12:58238923..58240450-chr12:58266214..58268296,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10431552	0.82[JPT][hapmap]
rs10444569	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783847	0.82[JPT][hapmap]
rs10783848	0.81[JPT][hapmap]
rs10783850	0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs10783851	0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs10783854	0.84[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783855	0.83[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10783856	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877012	0.82[JPT][hapmap]
rs10877014	0.82[JPT][hapmap]
rs10877015	0.82[JPT][hapmap]
rs10877016	0.82[JPT][hapmap]
rs10877019	0.82[JPT][hapmap]
rs10877024	0.87[AMR][1000 genomes]
rs10877025	0.87[AMR][1000 genomes]
rs10877026	0.86[AMR][1000 genomes]
rs10877028	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs10877029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172333	0.82[JPT][hapmap]
rs11172335	0.82[JPT][hapmap]
rs11172343	0.83[JPT][hapmap]
rs11172344	0.82[JPT][hapmap]
rs11172349	0.82[JPT][hapmap]
rs11172351	0.82[JPT][hapmap]
rs11172362	0.83[AMR][1000 genomes]
rs11172367	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.81[CEU][hapmap];0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172375	0.82[ASN][1000 genomes]
rs11172378	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs12312955	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12319233	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1599750	0.83[CEU][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599751	0.83[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875124	0.82[JPT][hapmap]
rs1875125	0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs1962047	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs3825079	0.82[JPT][hapmap]
rs4237844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646536	0.82[JPT][hapmap]
rs4760171	0.86[JPT][hapmap]
rs4760172	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760332	0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs4760335	0.81[AMR][1000 genomes]
rs4760340	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5017863	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59401446	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581155	0.82[JPT][hapmap]
rs6581157	0.84[ASN][1000 genomes]
rs703842	0.82[JPT][hapmap]
rs7134797	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7312623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489290	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs7969844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181644	0.82[JPT][hapmap]
rs870392	0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs871871	0.93[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	0.88[AMR][1000 genomes];0.98[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4760339	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4760339	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760339	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760339	METTL21B	cis	lung	GTEx
rs4760339	XRCC6BP1	cis	Whole Blood	GTEx
rs4760339	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760339	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs4760339	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760339	XRCC6BP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:43 , 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	chr12:58264000-58268600	Weak transcription	Placenta	Placenta
9	chr12:58264000-58269600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:58264400-58268600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:58264400-58269600	Weak transcription	Brain Substantia Nigra	brain
12	chr12:58264400-58269600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:58264400-58269800	Weak transcription	Brain Anterior Caudate	brain
14	chr12:58264600-58268400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:58267000-58269000	Enhancers	Right Atrium	heart
16	chr12:58267400-58268800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:58267400-58269000	Enhancers	Psoas Muscle	Psoas
18	chr12:58267600-58268400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr12:58267600-58268600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:58267600-58268600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:58267600-58268800	Enhancers	Brain Angular Gyrus	brain
22	chr12:58267600-58268800	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:58267600-58268800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr12:58267600-58269000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:58267600-58269000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr12:58267600-58269200	Enhancers	Colon Smooth Muscle	Colon
27	chr12:58267600-58270000	Enhancers	K562	blood
28	chr12:58267800-58268400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:58267800-58268400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:58267800-58268400	Enhancers	Fetal Muscle Leg	muscle
31	chr12:58267800-58268600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:58267800-58268600	Enhancers	Fetal Lung	lung
33	chr12:58267800-58268800	Enhancers	Colonic Mucosa	Colon
34	chr12:58267800-58268800	Enhancers	Fetal Stomach	stomach
35	chr12:58267800-58269000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:58267800-58269000	Enhancers	GM12878-XiMat	blood
37	chr12:58268000-58268400	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:58268000-58268400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:58268000-58268400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr12:58268000-58268800	Enhancers	Left Ventricle	heart
41	chr12:58268000-58268800	Enhancers	Rectal Smooth Muscle	rectum
42	chr12:58268000-58268800	Enhancers	Stomach Mucosa	stomach
43	chr12:58268000-58269400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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