Variant report

Variant	rs1040530
Chromosome Location	chr6:1758179-1758180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1755526..1758374-chr6:1765956..1768528,2	MCF-7	breast:
2	chr6:1756824..1758512-chr6:1760303..1761859,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1013303	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040528	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11242719	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12197874	0.80[ASN][1000 genomes]
rs12200248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206354	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2143402	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34669469	0.88[EUR][1000 genomes]
rs3734739	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734740	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734741	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800031	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3800032	0.81[JPT][hapmap]
rs3800033	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800034	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800035	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800036	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800038	0.80[CHB][hapmap]
rs3800040	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3800043	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs3823262	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140588	0.81[JPT][hapmap]
rs4546532	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959155	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959605	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959608	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61207262	0.83[EUR][1000 genomes]
rs6596848	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6596849	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6596850	0.92[ASN][1000 genomes]
rs6596853	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6596854	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6596855	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66477179	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67800638	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911480	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912189	0.93[ASN][1000 genomes]
rs6914704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6916153	0.96[ASN][1000 genomes]
rs6916760	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6933551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935246	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935905	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs742536	0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs761148	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7740666	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749846	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753928	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391929	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391930	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392332	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392333	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9392335	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9392336	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503018	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503019	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600809	chr6:1732741-1775436	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1040530	PSMG4	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1738400-1762400	Weak transcription	Gastric	stomach
2	chr6:1738400-1768200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:1749400-1761600	Weak transcription	Stomach Mucosa	stomach
4	chr6:1749800-1762400	Weak transcription	Colonic Mucosa	Colon
5	chr6:1749800-1779000	Weak transcription	Aorta	Aorta
6	chr6:1751200-1780400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:1756400-1760000	Strong transcription	HepG2	liver
8	chr6:1757000-1758200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:1757000-1766000	Weak transcription	Right Atrium	heart
10	chr6:1757200-1758200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:1757200-1760200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:1757200-1764000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:1757200-1766800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:1757200-1770600	Weak transcription	Lung	lung
15	chr6:1757600-1762800	Weak transcription	Pancreas	Pancrea
16	chr6:1757800-1758400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:1757800-1762200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:1758000-1759400	Weak transcription	Fetal Kidney	kidney

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