Variant report

Variant	rs28407987
Chromosome Location	chr3:56170504-56170505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13323783	0.89[EUR][1000 genomes]
rs13324556	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1452206	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1452207	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1519030	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1519031	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17056469	0.84[ASN][1000 genomes]
rs28397662	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28496913	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28583826	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28655135	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28689027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28780379	0.89[EUR][1000 genomes]
rs28888991	0.84[EUR][1000 genomes]
rs9311597	0.84[ASN][1000 genomes]
rs9810412	0.89[EUR][1000 genomes]
rs9815714	0.89[EUR][1000 genomes]
rs9816050	0.89[EUR][1000 genomes]
rs9818484	0.81[EUR][1000 genomes]
rs9821284	0.89[EUR][1000 genomes]
rs9824691	0.81[EUR][1000 genomes]
rs9830503	0.84[ASN][1000 genomes]
rs9834432	0.81[EUR][1000 genomes]
rs9834759	0.81[EUR][1000 genomes]
rs9840027	0.81[EUR][1000 genomes]
rs9842348	0.89[EUR][1000 genomes]
rs9843455	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9844377	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844806	0.84[EUR][1000 genomes]
rs9862097	0.84[ASN][1000 genomes]
rs9865282	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9867542	0.89[EUR][1000 genomes]
rs9867636	0.84[EUR][1000 genomes]
rs9878055	0.89[EUR][1000 genomes]
rs9879781	0.84[EUR][1000 genomes]
rs9880997	0.91[AMR][1000 genomes];0.81[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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56157800-56175400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56160000-56170600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56163000-56171400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:56165200-56170600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:56166400-56171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:56166400-56173600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:56166600-56171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:56167400-56170600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:56168200-56171000	Weak transcription	HUVEC	blood vessel
10	chr3:56168200-56171000	Weak transcription	NH-A	brain
11	chr3:56168200-56171600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:56168400-56171200	Weak transcription	HSMMtube	muscle
13	chr3:56168600-56171400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:56168800-56170600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:56168800-56170800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:56168800-56170800	Weak transcription	HSMM	muscle
17	chr3:56168800-56182400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:56170000-56170800	Enhancers	Ovary	ovary
19	chr3:56170000-56171400	Enhancers	A549	lung
20	chr3:56170200-56170600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:56170200-56170800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:56170200-56172000	Enhancers	Osteobl	bone
23	chr3:56170400-56170600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:56170400-56170800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:56170400-56171400	Weak transcription	HMEC	breast
26	chr3:56170400-56172000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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