Variant report

Variant	rs1337062
Chromosome Location	chr1:162063023-162063024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10157090	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10159401	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10458387	0.86[JPT][hapmap]
rs10458392	0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs10494366	0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10737536	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10753762	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10800298	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10800301	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800303	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10800305	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10800307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800311	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10918630	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10918671	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10918680	0.84[EUR][1000 genomes]
rs10918681	0.83[EUR][1000 genomes]
rs10918684	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10918687	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10918688	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10918740	0.87[MEX][hapmap]
rs11579080	0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11579850	0.85[EUR][1000 genomes]
rs11580365	0.85[EUR][1000 genomes]
rs11808624	0.83[EUR][1000 genomes]
rs12022557	0.86[JPT][hapmap]
rs12033159	0.92[ASN][1000 genomes]
rs12036268	0.92[ASN][1000 genomes]
rs12036529	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12144992	0.87[MEX][hapmap]
rs12406484	0.85[EUR][1000 genomes]
rs12406785	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12407513	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12727141	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12727810	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12733821	0.82[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1337060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];1.00[ASN][1000 genomes]
rs1415256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415257	0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1415258	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415259	0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415260	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415264	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1415265	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572498	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1572499	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1577771	0.92[ASN][1000 genomes]
rs2095626	0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2210942	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2225845	0.82[AMR][1000 genomes]
rs2225846	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2225847	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922867	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4098274	0.86[AMR][1000 genomes]
rs4656348	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4656349	0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4656350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];1.00[ASN][1000 genomes]
rs4656352	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657140	0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4657141	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657142	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4657143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657145	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4657150	0.87[MEX][hapmap]
rs4657152	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657154	0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657155	0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5000342	0.82[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6413902	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427650	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427651	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6664115	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672881	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6684179	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6684278	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6688966	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6696160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7417931	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7512106	0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7515045	0.86[JPT][hapmap]
rs7521236	0.85[EUR][1000 genomes]
rs7534045	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7538490	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541332	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7551959	0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7555508	0.80[AMR][1000 genomes]
rs945706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1821140	chr1:162047541-162389040	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv1818566	chr1:162061209-162430009	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv1823751	chr1:162063023-162344102	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv1821064	chr1:162063023-162363991	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1337062	COPA	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162041400-162063600	Weak transcription	Fetal Stomach	stomach
2	chr1:162059000-162063800	Weak transcription	Stomach Mucosa	stomach
3	chr1:162060800-162063200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:162060800-162063200	Enhancers	Liver	Liver
5	chr1:162060800-162064800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:162061400-162063200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:162061400-162063600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:162061800-162063200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:162061800-162064200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr1:162061800-162064400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:162062200-162063800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:162062200-162063800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:162062200-162064000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:162062200-162064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:162062200-162065800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:162062200-162069000	Weak transcription	Pancreas	Pancrea
17	chr1:162062400-162063400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:162062400-162063400	Weak transcription	Fetal Kidney	kidney
19	chr1:162062400-162063600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:162062600-162063200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:162062600-162063800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:162062600-162064800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:162062800-162063200	Enhancers	Aorta	Aorta
24	chr1:162062800-162063400	Enhancers	HSMMtube	muscle
25	chr1:162062800-162063800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:162063000-162063200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr1:162063000-162063200	Enhancers	Gastric	stomach
28	chr1:162063000-162063200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:162063000-162063400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr1:162063000-162063400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:162063000-162063600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:162063000-162064800	Enhancers	HepG2	liver
33	chr1:162063000-162068000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:162063000-162068000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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