Variant report

Variant	rs9491959
Chromosome Location	chr6:128790399-128790400
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1012629	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756545	1.00[ASN][1000 genomes]
rs17459694	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17460765	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17460940	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461178	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461290	0.91[AMR][1000 genomes]
rs1935130	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55848328	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62425728	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425730	1.00[ASN][1000 genomes]
rs62425732	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425734	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425736	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491965	0.81[EUR][1000 genomes]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9491959	PTPRK	cis	intralobular white matter	BrainEAC

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128773400-128795200	Weak transcription	HSMMtube	muscle
2	chr6:128778800-128790600	Weak transcription	Fetal Heart	heart
3	chr6:128780400-128795400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:128785600-128794400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128785600-128795200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:128785600-128795400	Weak transcription	A549	lung
7	chr6:128786200-128792800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:128786400-128792800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:128786400-128792800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:128786800-128795600	Weak transcription	HSMM	muscle
11	chr6:128787200-128792800	Weak transcription	Small Intestine	intestine
12	chr6:128787200-128794800	Weak transcription	Right Ventricle	heart
13	chr6:128787200-128795800	Weak transcription	Left Ventricle	heart
14	chr6:128787200-128795800	Weak transcription	Pancreas	Pancrea
15	chr6:128787400-128792800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:128787400-128793200	Weak transcription	Fetal Intestine Large	intestine
17	chr6:128787600-128790400	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:128787600-128794800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:128787600-128794800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:128787600-128795200	Weak transcription	NHEK	skin
21	chr6:128787600-128799200	Weak transcription	HepG2	liver
22	chr6:128787800-128792800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:128787800-128792800	Weak transcription	Fetal Intestine Small	intestine
24	chr6:128788000-128799000	Weak transcription	Liver	Liver
25	chr6:128788400-128795400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:128788800-128795000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:128790200-128790600	Enhancers	Stomach Mucosa	stomach
28	chr6:128790200-128791200	Enhancers	Brain Substantia Nigra	brain

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