Variant report

Variant	rs62253666
Chromosome Location	chr3:55930391-55930392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12108171	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633538	0.83[EUR][1000 genomes]
rs1458066	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17056061	0.80[AMR][1000 genomes]
rs17056065	0.82[ASN][1000 genomes]
rs17056081	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056090	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056098	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1902861	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55675302	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55682897	0.82[ASN][1000 genomes]
rs55724092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55967115	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55971093	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253660	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253661	0.88[EUR][1000 genomes]
rs62253664	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253667	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253668	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253669	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253670	0.82[EUR][1000 genomes]
rs62255832	0.80[AMR][1000 genomes]
rs62255835	0.82[ASN][1000 genomes]
rs62256771	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62256772	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62256773	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62256774	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62256778	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445755	0.82[ASN][1000 genomes]
rs6763408	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6766607	0.80[AMR][1000 genomes]
rs73073394	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73075332	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73075334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs733509	0.82[ASN][1000 genomes]
rs7618265	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7639013	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649504	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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	nsv876815	chr3:55895409-55979964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55920000-55931400	Weak transcription	Spleen	Spleen
2	chr3:55927800-55931400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:55927800-55932200	Weak transcription	HUVEC	blood vessel
4	chr3:55929400-55930600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:55929400-55932600	Enhancers	Brain Germinal Matrix	brain
6	chr3:55930000-55930400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:55930000-55930600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:55930000-55931800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:55930200-55930400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:55930200-55930600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:55930200-55930600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr3:55930200-55931000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:55930200-55931400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:55930200-55943200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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