Variant report

Variant	rs6781318
Chromosome Location	chr3:139101461-139101462
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	chr3:139091608..139097785-chr3:139099918..139103332,6	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513077	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11914638	1.00[CHB][hapmap]
rs11924964	1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928018	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107249	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599926	0.80[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289345	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2289346	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2307030	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34994114	0.94[ASN][1000 genomes]
rs56176652	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57459537	0.81[ASN][1000 genomes]
rs57490542	0.94[ASN][1000 genomes]
rs60077646	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61613815	0.94[ASN][1000 genomes]
rs6767503	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773840	1.00[ASN][1000 genomes]
rs6774691	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788896	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797945	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804069	0.88[AMR][1000 genomes]
rs72986758	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612306	0.94[ASN][1000 genomes]
rs7619827	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7649535	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651618	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9756378	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6781318	COPZ1	trans	parietal	SCAN

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	chr3:139065800-139101600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:139065800-139101600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:139065800-139102400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:139065800-139102400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:139065800-139102600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:139065800-139102800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:139065800-139103200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr3:139065800-139103600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:139065800-139104400	Strong transcription	Dnd41	blood
29	chr3:139066000-139101800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:139066000-139103600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:139066200-139102400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:139066200-139103800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:139066400-139102400	Strong transcription	Placenta	Placenta
34	chr3:139071200-139102200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:139072800-139101600	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr3:139073200-139102200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:139075000-139102200	Strong transcription	Adipose Nuclei	Adipose
38	chr3:139075200-139103800	Strong transcription	NHDF-Ad	bronchial
39	chr3:139078400-139104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:139078600-139102400	Strong transcription	GM12878-XiMat	blood
41	chr3:139081800-139102400	Strong transcription	NHLF	lung
42	chr3:139082200-139102400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:139084800-139107800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:139086000-139103000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:139086000-139104600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:139086400-139102400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:139086600-139102000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:139088200-139106000	Weak transcription	Stomach Mucosa	stomach
49	chr3:139092200-139107000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:139092200-139107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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