Variant report

Variant	rs804820
Chromosome Location	chr6:37584451-37584452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10947674	1.00[CHB][hapmap]
rs6901331	1.00[CHB][hapmap]
rs7751500	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804819	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs804853	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804854	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809251	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811703	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv602955	chr6:37581200-37599962	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs804820	PPIL1	cis	parietal	SCAN
rs804820	TREML2	cis	cerebellum	SCAN
rs804820	LHFPL5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37583200-37584600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr6:37583200-37584800	Enhancers	NH-A	brain
3	chr6:37583200-37587200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:37583600-37584600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:37583600-37587000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:37583800-37584600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:37583800-37584600	Enhancers	Hela-S3	cervix
8	chr6:37583800-37586600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:37584200-37584600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:37584200-37584800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr6:37584400-37584600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:37584400-37584600	Enhancers	Fetal Brain Male	brain
13	chr6:37584400-37584600	Bivalent Enhancer	K562	blood
14	chr6:37584400-37590600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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