Variant report

Variant	rs9399513
Chromosome Location	chr6:145193265-145193266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11546879	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13195905	0.86[JPT][hapmap]
rs13204600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13208243	1.00[MEX][hapmap]
rs13208561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13210728	0.86[JPT][hapmap]
rs13212915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213382	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13218938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1856418	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297844	0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs2297845	1.00[ASW][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs2297846	0.83[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs35415004	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36083145	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4476850	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs4495289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4642498	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9321993	0.91[JPT][hapmap]
rs9373428	0.91[JPT][hapmap]
rs9373431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376858	0.91[JPT][hapmap]
rs9390219	0.86[JPT][hapmap]
rs9390240	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390242	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399508	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399509	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403603	0.86[JPT][hapmap]
rs9403610	0.91[JPT][hapmap]
rs9403616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv886740	chr6:145105354-145199259	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv464070	chr6:145184504-145214952	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv604823	chr6:145184504-145214952	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv432966	chr6:145191307-145201307	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399513	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145189400-145194400	Weak transcription	Osteobl	bone
2	chr6:145189600-145195400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:145191800-145193400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:145192200-145194400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:145192400-145194400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:145192600-145193800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:145192600-145194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:145192800-145194200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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