Variant report

Variant	rs930019
Chromosome Location	chr2:64549033-64549034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1030408	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426704	0.87[GIH][hapmap];1.00[MKK][hapmap];0.86[ASN][1000 genomes]
rs1534684	0.84[EUR][1000 genomes]
rs2555417	0.84[EUR][1000 genomes]
rs2555424	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555429	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555431	0.92[ASN][1000 genomes]
rs2555432	0.92[ASN][1000 genomes]
rs2555447	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555450	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555451	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555454	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698540	0.92[ASN][1000 genomes]
rs6546066	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7560580	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562531	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573704	0.83[AMR][1000 genomes]
rs7582971	0.80[AMR][1000 genomes]
rs883021	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs930019	PELI1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64539800-64549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
3	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:64540800-64549600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
6	chr2:64543800-64549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:64546000-64552000	Weak transcription	Thymus	Thymus
8	chr2:64548200-64549400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:64549000-64549600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:64549000-64549800	Enhancers	Fetal Lung	lung
11	chr2:64549000-64550200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:64549000-64550800	Enhancers	Fetal Muscle Leg	muscle
13	chr2:64549000-64551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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