Variant report

Variant	rs1328366
Chromosome Location	chr13:93918144-93918145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1328370	0.88[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16948547	0.92[GIH][hapmap]
rs17188802	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17267523	0.88[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17645969	0.87[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs17645998	0.96[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs17702471	0.83[GIH][hapmap]
rs2209880	0.86[GIH][hapmap]
rs59772512	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61963740	0.81[AMR][1000 genomes]
rs61963741	0.81[AMR][1000 genomes]
rs61963744	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61963746	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61963747	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61963748	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61965664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61965665	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2751156	chr13:93912999-93988638	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1328366	GPC6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93897200-93923000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr13:93901400-93923400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:93903000-93922800	Weak transcription	Fetal Stomach	stomach
4	chr13:93903000-93923000	Weak transcription	Fetal Intestine Small	intestine
5	chr13:93910800-93920600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:93910800-93920800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:93911200-93922200	Weak transcription	HepG2	liver
8	chr13:93913600-93920400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:93913800-93920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr13:93914000-93921000	Weak transcription	A549	lung
11	chr13:93915400-93923200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:93916400-93922200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:93916600-93918600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:93917200-93921800	Strong transcription	hESC Derived CD184+ Endoderm 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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