Variant report

Variant	rs491409
Chromosome Location	chr1:76572360-76572361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11162082	0.83[AMR][1000 genomes]
rs12407026	0.83[AMR][1000 genomes]
rs12407031	0.83[AMR][1000 genomes]
rs12407845	0.83[AMR][1000 genomes]
rs12408886	1.00[JPT][hapmap]
rs12408918	1.00[JPT][hapmap]
rs158620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167050	0.83[EUR][1000 genomes]
rs17098119	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs172334	0.82[EUR][1000 genomes]
rs190861	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631779	1.00[JPT][hapmap]
rs289674	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289676	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289677	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289678	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289687	1.00[JPT][hapmap]
rs289692	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289693	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289700	0.83[EUR][1000 genomes]
rs289701	0.83[EUR][1000 genomes]
rs291059	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992503	0.83[EUR][1000 genomes]
rs3011994	0.83[EUR][1000 genomes]
rs3011995	0.80[EUR][1000 genomes]
rs35802431	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384233	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399529	0.85[EUR][1000 genomes]
rs403449	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447383	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs551954	0.95[EUR][1000 genomes]
rs552890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61558985	0.94[EUR][1000 genomes]
rs6593524	0.84[AMR][1000 genomes]
rs6664446	0.83[AMR][1000 genomes]
rs6673424	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6691344	0.82[AMR][1000 genomes]
rs915402	0.83[EUR][1000 genomes]
rs915403	0.83[EUR][1000 genomes]
rs915404	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:76557600-76588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:76560200-76573400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:76568600-76572400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:76569400-76572800	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:76569400-76573200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:76569400-76575400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:76570000-76573000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:76570000-76573600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:76570200-76573800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:76570600-76572800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:76570800-76574200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:76571000-76573000	Enhancers	Brain Hippocampus Middle	brain
15	chr1:76571000-76573800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:76571200-76575000	Weak transcription	Left Ventricle	heart
17	chr1:76571200-76575200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:76571200-76575400	Weak transcription	Fetal Lung	lung
19	chr1:76571400-76573000	Enhancers	Fetal Kidney	kidney
20	chr1:76571600-76572400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:76571800-76574200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:76571800-76575000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:76572000-76572800	Strong transcription	Primary B cells from cord blood	blood
24	chr1:76572000-76572800	Enhancers	Brain Anterior Caudate	brain
25	chr1:76572000-76574000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr1:76572000-76574200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:76572200-76573000	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:76572200-76573200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:76572200-76575000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:76572200-76575200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:76572200-76577000	Enhancers	Brain Substantia Nigra	brain

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