Variant report

Variant	rs12022557
Chromosome Location	chr1:162055584-162055585
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	chr1:162054073..162055694-chr1:162056144..162058969,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10157090	0.82[ASN][1000 genomes]
rs10159401	0.82[ASN][1000 genomes]
rs10458387	0.95[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10458392	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753762	0.83[ASN][1000 genomes]
rs10800301	0.87[ASN][1000 genomes]
rs10918615	0.84[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918630	0.93[ASN][1000 genomes]
rs10918738	0.88[ASN][1000 genomes]
rs11579080	0.95[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs12023182	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033159	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12036268	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12036529	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1337060	0.86[JPT][hapmap]
rs1337061	0.86[JPT][hapmap]
rs1337062	0.86[JPT][hapmap]
rs1415256	0.90[JPT][hapmap]
rs1415264	0.83[ASN][1000 genomes]
rs1415265	0.83[ASN][1000 genomes]
rs1415266	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1577771	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2225846	0.86[ASN][1000 genomes]
rs34578934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35021332	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4098274	0.96[ASN][1000 genomes]
rs4656348	0.88[ASN][1000 genomes]
rs4656349	0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4656350	0.86[JPT][hapmap]
rs4657141	0.86[JPT][hapmap]
rs4657152	0.83[ASN][1000 genomes]
rs4657154	0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4657155	0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs5000342	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs57398343	0.84[AFR][1000 genomes]
rs6413902	0.86[ASN][1000 genomes]
rs6427650	0.82[ASN][1000 genomes]
rs6427651	0.82[ASN][1000 genomes]
rs6664115	0.83[ASN][1000 genomes]
rs6684179	0.83[ASN][1000 genomes]
rs6684278	0.82[ASN][1000 genomes]
rs6696160	0.86[JPT][hapmap]
rs74127546	0.82[AFR][1000 genomes]
rs74127550	0.86[AFR][1000 genomes]
rs74127552	0.86[AFR][1000 genomes]
rs7512106	0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7515045	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs7534045	0.82[ASN][1000 genomes]
rs7538490	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7540690	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs945706	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12022557	COPA	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162041400-162063600	Weak transcription	Fetal Stomach	stomach
2	chr1:162044800-162056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:162045000-162056200	Weak transcription	Liver	Liver
4	chr1:162048000-162055600	Weak transcription	Aorta	Aorta
5	chr1:162048000-162056800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:162048800-162058400	Weak transcription	Left Ventricle	heart
7	chr1:162048800-162061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:162049800-162056800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:162050200-162058200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:162051200-162056800	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:162051200-162061600	Weak transcription	Brain Germinal Matrix	brain
12	chr1:162051400-162056400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:162051400-162056800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:162051400-162058200	Weak transcription	Stomach Mucosa	stomach
15	chr1:162051800-162061400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:162052000-162056600	Weak transcription	HUVEC	blood vessel
17	chr1:162052200-162062000	Weak transcription	Fetal Kidney	kidney
18	chr1:162054400-162058000	Weak transcription	Hela-S3	cervix
19	chr1:162055000-162056200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:162055200-162057200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:162055200-162061000	Enhancers	HepG2	liver

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