Variant report

Variant	rs1040641
Chromosome Location	chr6:164241690-164241691
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	chr6:164143541..164145828-chr6:164241681..164243954,2	K562	blood:
2	chr6:164240534..164242606-chr6:164247926..164250423,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10945921	0.81[CHB][hapmap]
rs1111705	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13203619	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2015261	0.96[ASN][1000 genomes]
rs2321978	0.85[CHB][hapmap]
rs2321979	0.81[CHB][hapmap]
rs4709760	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4709765	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709766	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4709769	0.81[CHB][hapmap]
rs4709773	0.83[ASN][1000 genomes]
rs6925383	0.93[ASN][1000 genomes]
rs7762180	0.92[ASN][1000 genomes]
rs7765258	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8180622	1.00[ASN][1000 genomes]
rs880095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295231	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295232	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295233	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9295234	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9346974	0.95[ASN][1000 genomes]
rs9346975	0.90[ASN][1000 genomes]
rs9347790	0.91[ASN][1000 genomes]
rs9347791	0.98[ASN][1000 genomes]
rs9347792	1.00[ASN][1000 genomes]
rs9347793	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347798	0.83[ASN][1000 genomes]
rs9355439	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9355440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9355441	0.81[CHB][hapmap]
rs9355442	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9356148	0.85[ASN][1000 genomes]
rs9356152	0.91[ASN][1000 genomes]
rs9356153	0.91[ASN][1000 genomes]
rs9356156	0.90[ASN][1000 genomes]
rs9364701	0.86[ASN][1000 genomes]
rs9364703	0.96[ASN][1000 genomes]
rs9365619	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9365620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9456883	0.88[ASN][1000 genomes]
rs9456885	1.00[AFR][1000 genomes];1.00[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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1040641	PACRG	cis	cerebellum	SCAN
rs1040641	NCRNA00241	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164230400-164249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:164236400-164249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:164236600-164241800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:164241000-164242600	Enhancers	Placenta	Placenta
5	chr6:164241000-164243400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:164241200-164242800	Enhancers	Brain Germinal Matrix	brain
7	chr6:164241600-164242000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:164241600-164243400	Enhancers	Fetal Brain Male	brain
9	chr6:164241600-164243400	Enhancers	Fetal Muscle Leg	muscle
10	chr6:164241600-164244000	Enhancers	Skeletal Muscle Female	skeletal muscle

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