Variant report

Variant	rs3850545
Chromosome Location	chr1:57577654-57577655
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11802124	1.00[AMR][1000 genomes]
rs155290	1.00[AMR][1000 genomes]
rs155292	1.00[AMR][1000 genomes]
rs17115034	1.00[AMR][1000 genomes]
rs1760208	1.00[AMR][1000 genomes]
rs498065	1.00[AMR][1000 genomes]
rs55750012	1.00[AMR][1000 genomes]
rs55891661	1.00[AMR][1000 genomes]
rs60411523	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61163916	1.00[AMR][1000 genomes]
rs72905258	1.00[AMR][1000 genomes]
rs72907176	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72917110	1.00[AMR][1000 genomes]
rs72919284	1.00[AMR][1000 genomes]
rs72919287	1.00[AMR][1000 genomes]
rs74074396	1.00[AMR][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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57574200-57578000	Enhancers	Fetal Heart	heart
3	chr1:57575000-57580600	Weak transcription	Left Ventricle	heart
4	chr1:57575000-57581600	Weak transcription	Right Atrium	heart
5	chr1:57575600-57580400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:57576200-57584800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:57576800-57579800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:57577000-57578200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:57577000-57578200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:57577000-57578200	Enhancers	HMEC	breast
11	chr1:57577000-57578600	Weak transcription	NHEK	skin
12	chr1:57577000-57578800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:57577000-57579800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:57577200-57595600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:57577400-57578600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:57577400-57578800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:57577600-57578200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:57577600-57578400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:57577600-57578800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:57577600-57578800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:57577600-57579400	Enhancers	HUES64 Cell Line	embryonic stem cell

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