Variant report

Variant	rs1415092
Chromosome Location	chr1:102462156-102462157
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10449717	0.91[ASN][1000 genomes]
rs11164369	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11591058	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118113	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120249	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140609	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12745544	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746978	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12747450	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1336794	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415095	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17434817	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2339204	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28541803	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2879370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34650715	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35337065	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4262563	0.91[ASN][1000 genomes]
rs4908204	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4908207	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6577293	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6577295	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7536265	0.91[ASN][1000 genomes]
rs7550681	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs945642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]

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	nsv522921	chr1:102170295-102876392	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv462628	chr1:102376258-102473559	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546900	chr1:102376258-102473559	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2422183	chr1:102450736-102796819	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1415092	GMDS	trans	lymphoblastoid	seeQTL
rs1415092	OLFM3	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:102460400-102463000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:102461000-102462800	Active TSS	Fetal Brain Female	brain
3	chr1:102461000-102463000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:102461400-102462200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr1:102461400-102462400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:102461400-102463000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:102461400-102463000	Active TSS	Brain Anterior Caudate	brain
8	chr1:102461400-102463000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr1:102461600-102462400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:102461600-102462400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:102461600-102462400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
12	chr1:102461600-102462600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:102461600-102462600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
14	chr1:102461600-102463000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:102461600-102463000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:102461600-102463000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:102461600-102463000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:102461600-102463000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr1:102461600-102463200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:102461800-102462200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr1:102461800-102462200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:102461800-102462200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:102461800-102462200	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr1:102461800-102462200	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
25	chr1:102461800-102462400	Bivalent Enhancer	Fetal Heart	heart
26	chr1:102461800-102462400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr1:102461800-102462400	Bivalent/Poised TSS	Fetal Kidney	kidney
28	chr1:102461800-102462600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:102461800-102462600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:102461800-102462600	Enhancers	Pancreas	Pancrea
31	chr1:102461800-102463000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:102461800-102463000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:102461800-102463000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:102461800-102463000	Active TSS	Fetal Brain Male	brain
35	chr1:102462000-102462200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:102462000-102462200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr1:102462000-102462200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:102462000-102462200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:102462000-102462200	Bivalent Enhancer	Fetal Lung	lung
40	chr1:102462000-102462200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr1:102462000-102462400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:102462000-102462400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:102462000-102462400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr1:102462000-102462600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:102462000-102462600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:102462000-102462600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
47	chr1:102462000-102462600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr1:102462000-102462800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:102462000-102462800	Enhancers	Right Atrium	heart

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