Variant report

Variant	rs486939
Chromosome Location	chr1:57576943-57576944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17453706	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471704	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs479075	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479780	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491585	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs499755	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs500614	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs506063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507709	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs514594	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs522532	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs536250	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552417	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs554637	0.90[EUR][1000 genomes]
rs556329	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560176	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs561503	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564575	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs564691	0.88[AFR][1000 genomes]
rs572427	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs573756	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6587763	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692939	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv526087	chr1:57576438-57579610	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57571600-57577600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:57571800-57577000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57572200-57577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:57573400-57577400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:57574200-57578000	Enhancers	Fetal Heart	heart
7	chr1:57574400-57577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:57575000-57580600	Weak transcription	Left Ventricle	heart
9	chr1:57575000-57581600	Weak transcription	Right Atrium	heart
10	chr1:57575600-57580400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:57576000-57577000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:57576200-57577600	Enhancers	Rectal Smooth Muscle	rectum
13	chr1:57576200-57584800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:57576600-57577400	Enhancers	Fetal Stomach	stomach
15	chr1:57576800-57577000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:57576800-57577000	Enhancers	NHEK	skin
17	chr1:57576800-57577200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:57576800-57577200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:57576800-57579800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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