Variant report

Variant	rs1434167
Chromosome Location	chr2:110396324-110396325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11541143	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2043462	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2060403	0.89[CEU][hapmap]
rs4312506	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953760	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs4953784	0.89[CEU][hapmap]
rs4953843	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4953850	0.80[EUR][1000 genomes]
rs56288075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594037	0.96[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs6594049	0.96[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs6723295	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6726252	0.90[GIH][hapmap];0.95[EUR][1000 genomes]
rs6748632	0.80[EUR][1000 genomes]
rs7596172	0.81[EUR][1000 genomes]
rs919941	0.96[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers 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	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1434167	ACOXL	cis	cerebellum	SCAN
rs1434167	C2orf26	cis	multi-tissue	Pritchard
rs1434167	SEPT10	cis	parietal	SCAN
rs1434167	SEPT10	cis	multi-tissue	Pritchard
rs1434167	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110392800-110396800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:110393800-110402200	Weak transcription	Fetal Thymus	thymus
3	chr2:110393800-110402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:110395000-110396800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:110395200-110396400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:110395200-110396800	Enhancers	Adipose Nuclei	Adipose
7	chr2:110395200-110396800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:110395400-110396400	Enhancers	NHEK	skin
9	chr2:110395400-110396800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:110395400-110396800	Enhancers	Hela-S3	cervix
11	chr2:110395400-110397000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:110395600-110396400	Enhancers	Liver	Liver
13	chr2:110395600-110396400	Enhancers	Osteobl	bone
14	chr2:110395600-110396600	Enhancers	Brain Hippocampus Middle	brain
15	chr2:110395600-110396600	Enhancers	Small Intestine	intestine
16	chr2:110395600-110396600	Flanking Active TSS	HepG2	liver
17	chr2:110395600-110396800	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:110396000-110396400	Enhancers	Brain Germinal Matrix	brain
19	chr2:110396000-110396400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:110396000-110396600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:110396200-110396400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:110396200-110396800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:110396200-110397000	Enhancers	GM12878-XiMat	blood
24	chr2:110396200-110397200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:110396200-110398000	Weak transcription	Placenta	Placenta
26	chr2:110396200-110401800	Weak transcription	Stomach Mucosa	stomach
27	chr2:110396200-110402200	Weak transcription	Lung	lung

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