Variant report

Variant	rs7765258
Chromosome Location	chr6:164214296-164214297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1040641	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1111705	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203619	0.82[ASN][1000 genomes]
rs2015261	0.88[ASN][1000 genomes]
rs4709760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709765	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4709766	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925383	0.86[ASN][1000 genomes]
rs7762180	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180622	0.91[ASN][1000 genomes]
rs880095	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295231	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295232	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295233	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9295234	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9346974	0.86[ASN][1000 genomes]
rs9346975	0.82[ASN][1000 genomes]
rs9347790	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9347791	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9347792	0.91[ASN][1000 genomes]
rs9347793	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9355439	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9355440	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9355442	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9356152	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356153	1.00[ASN][1000 genomes]
rs9356156	0.82[ASN][1000 genomes]
rs9364701	0.92[ASN][1000 genomes]
rs9364703	0.88[ASN][1000 genomes]
rs9365619	0.89[ASN][1000 genomes]
rs9365620	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9456883	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9456885	0.85[EUR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7765258	NCRNA00241	cis	cerebellum	SCAN
rs7765258	LPA	cis	cerebellum	SCAN
rs7765258	PACRG	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164210600-164214400	Weak transcription	GM12878-XiMat	blood
2	chr6:164211800-164214400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:164212000-164214600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:164212000-164214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:164212200-164214400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:164213400-164215400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:164213800-164214800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:164213800-164215000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:164213800-164215000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:164213800-164215000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:164213800-164215200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:164213800-164215400	Enhancers	HSMM	muscle
13	chr6:164214000-164214600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:164214000-164215000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:164214000-164215400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:164214200-164214400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:164214200-164214600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:164214200-164215000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:164214200-164215000	Enhancers	K562	blood
20	chr6:164214200-164215200	Enhancers	HSMMtube	muscle
21	chr6:164214200-164215200	Enhancers	NHDF-Ad	bronchial
22	chr6:164214200-164215400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:164214200-164215400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:164214200-164215400	Enhancers	NH-A	brain

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