Variant report

Variant	rs11265425
Chromosome Location	chr1:154245142-154245143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158820	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1044013	0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11265238	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11265251	0.95[JPT][hapmap]
rs11802893	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1194593	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1194596	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12023901	0.94[ASN][1000 genomes]
rs12025237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12026177	0.95[JPT][hapmap]
rs12026615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12027999	0.95[ASN][1000 genomes]
rs12028554	0.82[ASN][1000 genomes]
rs12028949	0.95[JPT][hapmap]
rs12043131	1.00[LWK][hapmap]
rs12062977	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12135346	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733060	0.96[ASN][1000 genomes]
rs12738393	0.96[ASN][1000 genomes]
rs12742691	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12743874	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12749447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12750321	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16835846	0.91[JPT][hapmap]
rs16835852	0.91[JPT][hapmap]
rs1760801	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1760802	0.95[JPT][hapmap]
rs1986709	0.82[ASN][1000 genomes]
rs2274993	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[ASN][1000 genomes]
rs2282227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340473	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2790689	0.81[JPT][hapmap]
rs2879788	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3762339	0.84[ASN][1000 genomes]
rs3762340	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3790613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3790614	0.96[ASN][1000 genomes]
rs3811453	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3811455	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3828077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3935419	0.95[JPT][hapmap]
rs4240871	0.82[ASN][1000 genomes]
rs4459102	0.81[JPT][hapmap]
rs4620534	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6427509	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6657214	0.82[ASN][1000 genomes]
rs6673752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6719	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7517578	0.81[ASN][1000 genomes]
rs7522777	0.83[ASN][1000 genomes]
rs9803857	0.95[JPT][hapmap]
rs9943093	0.84[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11265425	HAX1	cis	cerebellum	SCAN
rs11265425	S100A14	cis	cerebellum	SCAN
rs11265425	RAG1AP1	cis	cerebellum	SCAN
rs11265425	SPRR2B	cis	cerebellum	SCAN
rs11265425	LCE5A	cis	parietal	SCAN
rs11265425	HAX1	cis	lymphoblastoid	seeQTL
rs11265425	UBAP2L	cis	multi-tissue	Pritchard
rs11265425	C1orf43	cis	parietal	SCAN
rs11265425	HAX1	cis	multi-tissue	Pritchard
rs11265425	PYGO2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154244000-154246000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:154244200-154245200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:154244200-154245400	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:154244200-154245600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:154244200-154245600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:154244200-154245600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:154244200-154245600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:154244200-154245600	Active TSS	Hela-S3	cervix
9	chr1:154244200-154245800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:154244200-154245800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:154244200-154245800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:154244200-154245800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:154244200-154245800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:154244200-154245800	Active TSS	Fetal Brain Female	brain
15	chr1:154244200-154246000	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:154244200-154246200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:154244200-154246200	Active TSS	A549	lung
18	chr1:154244200-154246400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:154244400-154245200	Active TSS	Fetal Brain Male	brain
20	chr1:154244400-154245400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:154244400-154245400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:154244400-154245400	Active TSS	Brain Germinal Matrix	brain
23	chr1:154244400-154245400	Active TSS	Colonic Mucosa	Colon
24	chr1:154244400-154245400	Active TSS	Fetal Muscle Leg	muscle
25	chr1:154244400-154245400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:154244400-154245400	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:154244400-154245600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:154244400-154245600	Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:154244400-154245600	Active TSS	Brain Hippocampus Middle	brain
30	chr1:154244400-154245600	Active TSS	Fetal Intestine Large	intestine
31	chr1:154244400-154245600	Active TSS	Fetal Lung	lung
32	chr1:154244400-154245600	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:154244400-154245600	Active TSS	NH-A	brain
34	chr1:154244400-154245800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:154244400-154245800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:154244400-154245800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:154244400-154245800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:154244400-154245800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:154244400-154245800	Active TSS	Aorta	Aorta
40	chr1:154244400-154245800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:154244400-154245800	Active TSS	Ovary	ovary
42	chr1:154244400-154245800	Active TSS	Right Ventricle	heart
43	chr1:154244400-154245800	Active TSS	Thymus	Thymus
44	chr1:154244400-154245800	Active TSS	GM12878-XiMat	blood
45	chr1:154244400-154245800	Active TSS	K562	blood
46	chr1:154244400-154246000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:154244400-154246000	Active TSS	H9 Cell Line	embryonic stem cell
48	chr1:154244400-154246000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:154244400-154246000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:154244400-154246000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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