Variant report

Variant	rs413540
Chromosome Location	chr1:76575850-76575851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1335738	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172358	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs289679	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs289688	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs289689	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs289691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291060	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384639	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427589	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs441806	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs510025	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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
3	nsv518927	chr1:76573614-76586272	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv522056	chr1:76573614-76598209	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 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	chr1:76572200-76577000	Enhancers	Brain Substantia Nigra	brain
5	chr1:76573400-76576400	Enhancers	Brain Angular Gyrus	brain
6	chr1:76574000-76576800	Enhancers	Brain Anterior Caudate	brain
7	chr1:76574800-76576400	Enhancers	Adipose Nuclei	Adipose
8	chr1:76575000-76576000	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:76575000-76576000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:76575000-76576600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:76575000-76577000	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:76575200-76576000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:76575200-76576400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:76575200-76576400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:76575200-76576800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:76575400-76576200	Weak transcription	Left Ventricle	heart
17	chr1:76575400-76576200	Weak transcription	Lung	lung
18	chr1:76575400-76576200	Weak transcription	Pancreas	Pancrea
19	chr1:76575400-76576400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:76575400-76576400	Enhancers	Fetal Lung	lung
21	chr1:76575400-76576800	Enhancers	Brain Hippocampus Middle	brain
22	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:76575600-76576600	Enhancers	Primary B cells from cord blood	blood
24	chr1:76575600-76579200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:76575800-76576200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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