Variant report

Variant	rs4406141
Chromosome Location	chr9:108327505-108327506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10069510	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741075	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12110137	0.84[EUR][1000 genomes]
rs13162651	0.83[EUR][1000 genomes]
rs13175193	0.83[EUR][1000 genomes]
rs1351720	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1384732	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483303	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2005147	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2580258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2589181	0.82[ASN][1000 genomes]
rs2696013	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2878967	0.81[ASN][1000 genomes]
rs4133429	0.84[EUR][1000 genomes]
rs56908114	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414906	0.84[EUR][1000 genomes]
rs6451801	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6451804	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451807	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451810	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451812	0.83[EUR][1000 genomes]
rs6860200	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892290	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892594	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6892627	0.83[EUR][1000 genomes]
rs6893773	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7446182	0.84[EUR][1000 genomes]
rs755048	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4406141	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321200-108335600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:108321600-108336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:108321600-108354000	Weak transcription	Right Ventricle	heart
8	chr9:108321600-108360200	Weak transcription	HSMM	muscle
9	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:108322200-108334600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:108324600-108334400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:108324800-108353800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:108325400-108327800	Weak transcription	Primary B cells from cord blood	blood
14	chr9:108325400-108334600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:108325400-108335000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:108325400-108337800	Weak transcription	Dnd41	blood
17	chr9:108325400-108339200	Weak transcription	Fetal Brain Male	brain
18	chr9:108325400-108357200	Weak transcription	A549	lung
19	chr9:108325600-108336600	Weak transcription	Fetal Lung	lung
20	chr9:108325600-108353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:108325600-108353200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:108325600-108353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:108325800-108353800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:108326000-108334000	Weak transcription	Left Ventricle	heart
25	chr9:108326000-108334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:108326000-108338200	Weak transcription	Ovary	ovary

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