Variant report

Variant	rs9380741
Chromosome Location	chr6:38352079-38352080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38351204..38353716-chr6:38356621..38358172,2	MCF-7	breast:
2	chr6:38350378..38352979-chr6:38364532..38367157,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12208912	0.85[JPT][hapmap]
rs12215330	0.85[JPT][hapmap]
rs1983605	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2294739	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140443	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711538	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711540	0.87[EUR][1000 genomes]
rs4711541	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711543	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711546	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs4714149	0.82[CHB][hapmap]
rs4714151	0.89[EUR][1000 genomes]
rs4714152	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs4714153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714155	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4714156	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714157	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4714158	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs58424668	0.87[EUR][1000 genomes]
rs58807047	0.87[EUR][1000 genomes]
rs6903060	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6903611	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6903767	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6923701	0.96[EUR][1000 genomes]
rs742515	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7743023	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748599	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs7749685	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7756267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7759078	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]
rs7759629	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7764502	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7766214	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9296248	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9296249	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9349076	0.97[EUR][1000 genomes]
rs9349077	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9349078	0.96[EUR][1000 genomes]
rs9349079	0.96[EUR][1000 genomes]
rs9357269	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9357270	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9357271	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9357272	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9366957	0.85[EUR][1000 genomes]
rs9366959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366960	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9369055	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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369057	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9380740	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380742	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9380743	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9380745	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9380747	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[EUR][1000 genomes]
rs9394493	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394494	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]
rs9470865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470867	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9470868	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9470874	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9380741	GLO1	cis	parietal	SCAN
rs9380741	TDRG1	cis	cerebellum	SCAN
rs9380741	PACSIN1	cis	cerebellum	SCAN
rs9380741	KCNK5	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38343000-38367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:38343400-38354600	Weak transcription	NHDF-Ad	bronchial
3	chr6:38350200-38366200	Weak transcription	Lung	lung
4	chr6:38351800-38356000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:38352000-38353000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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