Variant report

Variant	rs476258
Chromosome Location	chr11:77097793-77097794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1225478	0.88[EUR][1000 genomes]
rs1237490	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2154754	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2602460	0.81[ASN][1000 genomes]
rs2602461	0.80[ASN][1000 genomes]
rs2602462	0.80[ASN][1000 genomes]
rs2602474	0.80[ASN][1000 genomes]
rs2602475	0.82[ASN][1000 genomes]
rs2602476	0.86[EUR][1000 genomes]
rs2602487	0.83[EUR][1000 genomes]
rs2729749	0.81[ASN][1000 genomes]
rs2729751	0.81[ASN][1000 genomes]
rs2729775	0.82[ASN][1000 genomes]
rs2844335	0.83[ASN][1000 genomes]
rs2852381	0.82[ASN][1000 genomes]
rs2852383	0.81[ASN][1000 genomes]
rs2852388	0.83[ASN][1000 genomes]
rs2853084	0.82[ASN][1000 genomes]
rs2853091	0.82[ASN][1000 genomes]
rs2853098	0.80[ASN][1000 genomes]
rs3015982	0.86[EUR][1000 genomes]
rs3015983	0.84[EUR][1000 genomes]
rs3015985	0.84[EUR][1000 genomes]
rs3015986	0.83[EUR][1000 genomes]
rs3015988	0.83[EUR][1000 genomes]
rs3015990	0.83[EUR][1000 genomes]
rs3019233	0.85[EUR][1000 genomes]
rs3019234	0.85[EUR][1000 genomes]
rs3019235	0.84[EUR][1000 genomes]
rs3019236	0.85[EUR][1000 genomes]
rs3019249	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3019257	0.84[EUR][1000 genomes]
rs34880271	0.88[EUR][1000 genomes]
rs472691	0.88[EUR][1000 genomes]
rs473012	0.83[AFR][1000 genomes]
rs478134	0.80[AFR][1000 genomes]
rs479104	0.86[EUR][1000 genomes]
rs492527	0.83[AFR][1000 genomes]
rs493256	0.88[EUR][1000 genomes]
rs494289	0.85[EUR][1000 genomes]
rs497946	0.80[AFR][1000 genomes]
rs503406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs505841	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs508662	0.88[EUR][1000 genomes]
rs51500	0.88[EUR][1000 genomes]
rs520938	0.81[EUR][1000 genomes]
rs522015	0.89[EUR][1000 genomes]
rs523481	0.89[EUR][1000 genomes]
rs531638	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs535008	0.88[EUR][1000 genomes]
rs539906	0.80[AFR][1000 genomes]
rs552323	0.89[EUR][1000 genomes]
rs557484	0.88[EUR][1000 genomes]
rs558470	0.88[EUR][1000 genomes]
rs560571	0.86[EUR][1000 genomes]
rs561153	0.80[AFR][1000 genomes]
rs561386	0.89[EUR][1000 genomes]
rs562845	0.88[EUR][1000 genomes]
rs562939	0.80[AFR][1000 genomes]
rs563731	0.88[EUR][1000 genomes]
rs568309	0.83[AFR][1000 genomes]
rs572485	0.88[EUR][1000 genomes]
rs575662	0.80[AFR][1000 genomes]
rs576220	0.87[EUR][1000 genomes]
rs580624	0.89[EUR][1000 genomes]
rs584909	0.80[AFR][1000 genomes]
rs592602	0.84[EUR][1000 genomes]
rs595654	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs598801	0.88[EUR][1000 genomes]
rs605910	0.80[AFR][1000 genomes]
rs635291	0.80[AFR][1000 genomes]
rs644551	0.89[EUR][1000 genomes]
rs649040	0.89[EUR][1000 genomes]
rs653792	0.88[EUR][1000 genomes]
rs674259	0.89[EUR][1000 genomes]
rs683455	0.87[EUR][1000 genomes]
rs683762	0.88[EUR][1000 genomes]
rs684793	0.87[EUR][1000 genomes]
rs686068	0.88[EUR][1000 genomes]
rs689108	0.86[EUR][1000 genomes]
rs7105662	0.81[ASN][1000 genomes]
rs724369	0.82[ASN][1000 genomes]
rs7934230	0.83[EUR][1000 genomes]
rs7949721	0.82[EUR][1000 genomes]
rs98703	0.83[AFR][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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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
rs476258	PAK1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
3	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
4	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:77082400-77104200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:77084400-77103600	Weak transcription	Fetal Kidney	kidney
10	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
11	chr11:77086400-77108000	Weak transcription	Brain Anterior Caudate	brain
12	chr11:77086600-77102200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:77086600-77120000	Weak transcription	Spleen	Spleen
14	chr11:77087200-77106800	Weak transcription	NHEK	skin
15	chr11:77089400-77101200	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:77090800-77103000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:77090800-77103200	Weak transcription	Liver	Liver
18	chr11:77090800-77104200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:77090800-77104400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:77090800-77106400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:77090800-77111200	Weak transcription	HMEC	breast
22	chr11:77091000-77098600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:77091000-77103600	Weak transcription	Aorta	Aorta
24	chr11:77091000-77103800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:77091000-77104000	Weak transcription	Fetal Brain Male	brain
26	chr11:77091000-77106800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:77091000-77108200	Weak transcription	Brain Angular Gyrus	brain
28	chr11:77091000-77112000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:77091000-77113400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:77091000-77117000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:77091000-77117600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:77091200-77099800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:77091800-77106800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:77092000-77106800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:77092400-77103400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:77093600-77102000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:77093600-77102000	Weak transcription	HSMM	muscle
38	chr11:77093600-77104000	Weak transcription	Osteobl	bone
39	chr11:77093600-77117800	Weak transcription	NH-A	brain
40	chr11:77094000-77104400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:77094000-77118400	Weak transcription	NHLF	lung
42	chr11:77094200-77100200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr11:77094200-77102000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:77094200-77103400	Weak transcription	Adipose Nuclei	Adipose
45	chr11:77094200-77111800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr11:77094200-77118200	Weak transcription	NHDF-Ad	bronchial
47	chr11:77094200-77118400	Weak transcription	Colonic Mucosa	Colon
48	chr11:77094400-77104400	Weak transcription	Small Intestine	intestine
49	chr11:77095000-77101200	Weak transcription	Fetal Intestine Small	intestine
50	chr11:77095400-77101200	Weak transcription	Fetal Intestine Large	intestine

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