Variant report

Variant	rs4143771
Chromosome Location	chr6:28664631-28664632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12180700	0.88[EUR][1000 genomes]
rs1319075	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1337585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394149	0.89[EUR][1000 genomes]
rs4289643	0.81[EUR][1000 genomes]
rs6456831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6902736	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6925714	0.86[EUR][1000 genomes]
rs7381993	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7382112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7382146	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7383248	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7748643	0.94[AFR][1000 genomes]
rs7752875	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9378185	0.85[EUR][1000 genomes]
rs9380083	0.85[EUR][1000 genomes]
rs9393921	0.85[EUR][1000 genomes]
rs9885928	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4143771	ZSCAN23	cis	parietal	SCAN
rs4143771	ZSCAN23	cis	cerebellum	SCAN
rs4143771	ZNF192	cis	cerebellum	SCAN
rs4143771	ZKSCAN3	cis	parietal	SCAN
rs4143771	ZNF187	cis	cerebellum	SCAN
rs4143771	HIST1H2BL	cis	cerebellum	SCAN
rs4143771	ZKSCAN3	cis	cerebellum	SCAN
rs4143771	ZNF323	cis	cerebellum	SCAN
rs4143771	ZNF323	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28658200-28667400	Weak transcription	K562	blood
2	chr6:28661000-28665000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28663000-28667400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28663200-28664800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:28663400-28664800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:28663600-28664800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28663800-28664800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:28663800-28664800	Active TSS	Right Atrium	heart
9	chr6:28664600-28664800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
10	chr6:28664600-28664800	Flanking Bivalent TSS/Enh	HepG2	liver

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Input of quick search could be:

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

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