Variant report

Variant	rs6539102
Chromosome Location	chr12:104227844-104227845
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104227614..104228508-chr14:65436977..65437892,2	MCF-7	breast:
2	chr12:104215538..104217746-chr12:104226059..104228038,3	K562	blood:
3	chr12:104226575..104228496-chr12:104456969..104459135,2	K562	blood:
4	chr12:104226766..104229237-chr12:104233680..104235208,2	MCF-7	breast:
5	chr12:104193794..104196589-chr12:104226529..104230835,4	MCF-7	breast:
6	chr12:104200257..104201924-chr12:104226182..104228413,2	K562	blood:
7	chr12:104227204..104231494-chr12:104232251..104237257,7	MCF-7	breast:
8	chr12:104192744..104195300-chr12:104227670..104230455,2	MCF-7	breast:
9	chr12:104206137..104208857-chr12:104227836..104229349,2	K562	blood:
10	chr12:104218296..104220152-chr12:104227308..104229247,2	K562	blood:
11	chr12:104226069..104228785-chr12:104231042..104233623,3	MCF-7	breast:
12	chr12:104198918..104202818-chr12:104225755..104230550,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10082821	0.83[EUR][1000 genomes]
rs10778288	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10778289	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861111	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861113	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861115	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10861117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861118	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861119	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111780	0.92[ASN][1000 genomes]
rs11111790	0.83[EUR][1000 genomes]
rs11111794	0.90[EUR][1000 genomes]
rs11111797	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111803	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11111807	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12299784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12312058	0.86[ASN][1000 genomes]
rs12320424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12369835	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370782	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370783	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17034527	0.91[ASN][1000 genomes]
rs17034633	0.90[ASN][1000 genomes]
rs17034635	0.90[ASN][1000 genomes]
rs17034657	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964197	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964787	0.91[EUR][1000 genomes]
rs57412476	0.91[ASN][1000 genomes]
rs57498429	0.91[ASN][1000 genomes]
rs57739230	0.86[ASN][1000 genomes]
rs59509226	0.90[ASN][1000 genomes]
rs60828015	0.92[ASN][1000 genomes]
rs7132446	0.90[ASN][1000 genomes]
rs7135803	0.90[ASN][1000 genomes]
rs7315948	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73175816	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs884394	0.96[ASN][1000 genomes]
rs934844	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539102	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104218400-104233000	Weak transcription	Gastric	stomach
2	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
4	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:104222200-104232200	Weak transcription	NHLF	lung
7	chr12:104222400-104228800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:104222600-104232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:104223200-104233000	Weak transcription	HSMMtube	muscle
10	chr12:104223800-104232000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:104224600-104229400	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:104225000-104228800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:104225000-104233600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:104225200-104233200	Weak transcription	Right Atrium	heart
15	chr12:104225400-104228800	Enhancers	Colon Smooth Muscle	Colon
16	chr12:104225600-104233000	Weak transcription	Placenta	Placenta
17	chr12:104226200-104228000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:104226200-104228000	Enhancers	Fetal Lung	lung
19	chr12:104226400-104228000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:104226400-104228000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:104226400-104228400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:104226400-104228400	Enhancers	NHDF-Ad	bronchial
23	chr12:104226400-104228600	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:104226400-104229000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:104226400-104229000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:104226600-104228000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr12:104226600-104228400	Enhancers	Osteobl	bone
28	chr12:104226600-104229200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:104226600-104232000	Weak transcription	Stomach Mucosa	stomach
30	chr12:104226800-104232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:104226800-104233200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:104227000-104228800	Weak transcription	GM12878-XiMat	blood
33	chr12:104227000-104228800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr12:104227200-104228200	Weak transcription	Primary B cells from cord blood	blood
35	chr12:104227200-104228800	Enhancers	HMEC	breast
36	chr12:104227400-104228000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:104227400-104228000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:104227400-104228000	Enhancers	Fetal Stomach	stomach
39	chr12:104227400-104228800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:104227400-104228800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:104227400-104229000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:104227400-104229000	Enhancers	HSMM	muscle
43	chr12:104227400-104229400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:104227400-104229800	Flanking Active TSS	K562	blood
45	chr12:104227400-104230000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:104227400-104231200	Enhancers	HepG2	liver
47	chr12:104227600-104228000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:104227600-104228000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:104227600-104228000	Enhancers	Ovary	ovary
50	chr12:104227600-104228000	Enhancers	NHEK	skin

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