Variant report

Variant	rs4964571
Chromosome Location	chr12:104227273-104227274
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr12:104226575..104228496-chr12:104456969..104459135,2	K562	blood:
5	chr12:104226766..104229237-chr12:104233680..104235208,2	MCF-7	breast:
6	chr12:104193794..104196589-chr12:104226529..104230835,4	MCF-7	breast:
7	chr12:104200257..104201924-chr12:104226182..104228413,2	K562	blood:
8	chr12:104227204..104231494-chr12:104232251..104237257,7	MCF-7	breast:
9	chr12:104226069..104228785-chr12:104231042..104233623,3	MCF-7	breast:
10	chr12:104198918..104202818-chr12:104225755..104230550,5	K562	blood:

No data

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

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10082821	0.83[EUR][1000 genomes]
rs10778288	0.93[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10778289	0.93[CEU][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	0.91[CEU][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs11111794	0.90[EUR][1000 genomes]
rs11111797	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111803	0.93[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111806	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12312058	0.86[ASN][1000 genomes]
rs12313259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12320424	1.00[CEU][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17034633	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17034635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17034657	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964197	0.86[CEU][hapmap];0.90[TSI][hapmap];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]
rs4964574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964605	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964787	0.86[CEU][hapmap];1.00[TSI][hapmap];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]
rs6539102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132446	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7135803	0.90[ASN][1000 genomes]
rs7315948	0.86[CEU][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73175816	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs884394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs934844	1.00[CHB][hapmap];1.00[JPT][hapmap];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
rs4964571	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:59 , 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	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:104222200-104227400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:104222200-104232200	Weak transcription	NHLF	lung
13	chr12:104222400-104227400	Weak transcription	HSMM	muscle
14	chr12:104222400-104228800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:104222600-104232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:104223200-104227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:104223200-104233000	Weak transcription	HSMMtube	muscle
18	chr12:104223800-104232000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:104224400-104227600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:104224600-104229400	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:104225000-104228800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:104225000-104233600	Weak transcription	Primary T cells from cord blood	blood
23	chr12:104225200-104233200	Weak transcription	Right Atrium	heart
24	chr12:104225400-104228800	Enhancers	Colon Smooth Muscle	Colon
25	chr12:104225600-104227600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:104225600-104227600	Weak transcription	Aorta	Aorta
27	chr12:104225600-104233000	Weak transcription	Placenta	Placenta
28	chr12:104225800-104227400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:104226000-104227800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:104226200-104227600	Weak transcription	NHEK	skin
31	chr12:104226200-104228000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:104226200-104228000	Enhancers	Fetal Lung	lung
33	chr12:104226400-104228000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:104226400-104228000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:104226400-104228400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:104226400-104228400	Enhancers	NHDF-Ad	bronchial
37	chr12:104226400-104228600	Enhancers	Rectal Smooth Muscle	rectum
38	chr12:104226400-104229000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:104226400-104229000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:104226600-104227400	Weak transcription	HepG2	liver
41	chr12:104226600-104227600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:104226600-104227600	Weak transcription	Ovary	ovary
43	chr12:104226600-104227800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:104226600-104228000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:104226600-104228400	Enhancers	Osteobl	bone
46	chr12:104226600-104229200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:104226600-104232000	Weak transcription	Stomach Mucosa	stomach
48	chr12:104226800-104227400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:104226800-104227400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:104226800-104227400	Enhancers	K562	blood

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