Variant report

Variant	rs11264824
Chromosome Location	chr1:153973171-153973172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12032227	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12033532	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12042836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043354	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2072704	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2297895	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs2790688	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2790689	0.86[JPT][hapmap]
rs34752019	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs4459102	0.86[JPT][hapmap]
rs61805529	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671009	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs9700537	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11264824	HAX1	cis	parietal	SCAN
rs11264824	SLC27A3	cis	lymphoblastoid	seeQTL
rs11264824	HAX1	cis	lymphoblastoid	seeQTL
rs11264824	HAX1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153965600-153974000	Weak transcription	NHLF	lung
2	chr1:153965600-153975000	Weak transcription	Fetal Brain Male	brain
3	chr1:153966800-153973400	Weak transcription	HSMMtube	muscle
4	chr1:153966800-153973400	Weak transcription	NHDF-Ad	bronchial
5	chr1:153966800-153974000	Weak transcription	HSMM	muscle
6	chr1:153966800-153974200	Weak transcription	HMEC	breast
7	chr1:153966800-153974400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:153966800-153978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:153967000-153974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:153967000-153974200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:153967000-153983600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:153967200-153976000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:153967600-153974200	Weak transcription	NHEK	skin
14	chr1:153967800-153974400	Weak transcription	Gastric	stomach
15	chr1:153967800-153977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:153968200-153974200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:153968200-153974400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:153968400-153973400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:153968400-153973800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:153968400-153973800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:153968400-153974000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:153968400-153974000	Weak transcription	Osteobl	bone
23	chr1:153968400-153974200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:153968400-153974200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:153968400-153974400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:153968400-153974600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:153968400-153976000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:153968400-153976400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:153968400-153978200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:153968400-153978200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:153968400-153978600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:153968400-153986200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:153968400-153987000	Weak transcription	Brain Anterior Caudate	brain
34	chr1:153968400-153988400	Weak transcription	Primary B cells from cord blood	blood
35	chr1:153968800-153974200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:153968800-153976200	Weak transcription	Fetal Brain Female	brain
37	chr1:153972800-153973600	Strong transcription	Brain Substantia Nigra	brain
38	chr1:153972800-153974000	Enhancers	HepG2	liver
39	chr1:153972800-153974800	Enhancers	Fetal Heart	heart
40	chr1:153972800-153975400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:153973000-153973200	Enhancers	NH-A	brain
42	chr1:153973000-153974200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:153973000-153974600	Enhancers	Stomach Mucosa	stomach
44	chr1:153973000-153975400	Enhancers	Placenta	Placenta

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