Variant report

Variant	rs12299784
Chromosome Location	chr12:104226280-104226281
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104207300..104208804-chr12:104224699..104227695,2	K562	blood:
2	chr12:104206123..104208804-chr12:104221926..104227695,4	K562	blood:
3	chr12:104215538..104217746-chr12:104226059..104228038,3	K562	blood:
4	chr12:104200257..104201924-chr12:104226182..104228413,2	K562	blood:
5	chr12:104192629..104194904-chr12:104224915..104226874,2	MCF-7	breast:
6	chr12:104226069..104228785-chr12:104231042..104233623,3	MCF-7	breast:
7	chr12:104198918..104202818-chr12:104225755..104230550,5	K562	blood:

No data

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082821	0.82[EUR][1000 genomes]
rs10778288	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10778289	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861111	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861113	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861115	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861118	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861119	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111790	0.82[EUR][1000 genomes]
rs11111794	0.89[EUR][1000 genomes]
rs11111797	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111803	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111807	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12313259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12320424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369835	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370782	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1370783	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17034633	0.82[ASN][1000 genomes]
rs17034635	0.82[ASN][1000 genomes]
rs17034657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964197	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964571	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4964574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964787	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs59509226	0.82[ASN][1000 genomes]
rs6539102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7132446	0.82[ASN][1000 genomes]
rs7135803	0.82[ASN][1000 genomes]
rs7315948	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73175816	0.85[AMR][1000 genomes];0.90[EUR][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
rs12299784	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
2	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:104216600-104227800	Weak transcription	NH-A	brain
5	chr12:104218400-104233000	Weak transcription	Gastric	stomach
6	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:104218800-104227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
9	chr12:104219600-104226400	Weak transcription	Ovary	ovary
10	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:104222200-104226400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:104222200-104226600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:104222200-104227400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:104222200-104232200	Weak transcription	NHLF	lung
16	chr12:104222400-104226400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:104222400-104226600	Weak transcription	Osteobl	bone
18	chr12:104222400-104227400	Weak transcription	HSMM	muscle
19	chr12:104222400-104228800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:104222600-104232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:104222800-104226800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:104223000-104226600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:104223200-104226400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:104223200-104226400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:104223200-104227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:104223200-104233000	Weak transcription	HSMMtube	muscle
27	chr12:104223400-104226400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:104223400-104226600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:104223400-104226600	Weak transcription	HMEC	breast
30	chr12:104223800-104232000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:104224400-104227600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:104224600-104229400	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:104225000-104226600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:104225000-104228800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:104225000-104233600	Weak transcription	Primary T cells from cord blood	blood
36	chr12:104225200-104233200	Weak transcription	Right Atrium	heart
37	chr12:104225400-104226600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:104225400-104228800	Enhancers	Colon Smooth Muscle	Colon
39	chr12:104225600-104226800	Weak transcription	K562	blood
40	chr12:104225600-104227600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:104225600-104227600	Weak transcription	Aorta	Aorta
42	chr12:104225600-104233000	Weak transcription	Placenta	Placenta
43	chr12:104225800-104226400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:104225800-104226800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:104225800-104227000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:104225800-104227400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:104226000-104226400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:104226000-104226600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:104226000-104226600	Enhancers	HepG2	liver
50	chr12:104226000-104226800	Enhancers	Primary hematopoietic stem cells	blood

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