Variant report

Variant	rs13060697
Chromosome Location	chr3:139101777-139101778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139095204..139096886-chr3:139101729..139104066,2	K562	blood:
2	chr3:139091608..139097785-chr3:139099918..139103332,6	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044826	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10460845	0.84[ASN][1000 genomes]
rs10935320	0.92[ASN][1000 genomes]
rs10935323	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488939	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12494556	0.86[AMR][1000 genomes]
rs12494806	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695698	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12695699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12695700	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13071857	0.82[EUR][1000 genomes]
rs13074208	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13083195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085888	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13089007	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13089052	0.87[AMR][1000 genomes]
rs13089090	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13092507	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13092935	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1586861	0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1586863	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1586864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17336869	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1907687	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2349059	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34623690	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772879	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4407373	0.80[YRI][hapmap]
rs4544576	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683818	0.86[AMR][1000 genomes]
rs67929453	0.93[ASN][1000 genomes]
rs7374385	0.92[EUR][1000 genomes]
rs747346	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs964227	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs973691	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9812192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9818691	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825064	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9835241	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9848241	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849039	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9849578	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853350	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860201	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860521	0.86[AMR][1000 genomes]
rs9868544	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9882014	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:139065000-139103800	Strong transcription	HSMM	muscle
3	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:139065400-139102600	Strong transcription	Osteobl	bone
10	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
12	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
17	chr3:139065600-139103600	Strong transcription	NH-A	brain
18	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:139065800-139102400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:139065800-139102400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:139065800-139102600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:139065800-139102800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:139065800-139103200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr3:139065800-139103600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:139065800-139104400	Strong transcription	Dnd41	blood
27	chr3:139066000-139101800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:139066000-139103600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr3:139066200-139102400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:139066200-139103800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:139066400-139102400	Strong transcription	Placenta	Placenta
32	chr3:139071200-139102200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:139073200-139102200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr3:139075000-139102200	Strong transcription	Adipose Nuclei	Adipose
35	chr3:139075200-139103800	Strong transcription	NHDF-Ad	bronchial
36	chr3:139078400-139104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:139078600-139102400	Strong transcription	GM12878-XiMat	blood
38	chr3:139081800-139102400	Strong transcription	NHLF	lung
39	chr3:139082200-139102400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:139084800-139107800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:139086000-139103000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:139086000-139104600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:139086400-139102400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:139086600-139102000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:139088200-139106000	Weak transcription	Stomach Mucosa	stomach
46	chr3:139092200-139107000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:139092200-139107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:139092400-139107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:139093000-139106200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:139095000-139107000	Weak transcription	Esophagus	oesophagus

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