Variant report

Variant	rs7188650
Chromosome Location	chr16:81314381-81314382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000103121	Chromatin interaction
ENSG00000260495	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000261609	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11647597	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12449108	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921896	0.91[ASN][1000 genomes]
rs35552299	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3803651	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4888133	0.82[EUR][1000 genomes]
rs7192773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7194812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7194998	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7499777	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7500996	0.81[MEX][hapmap]
rs8047137	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9927546	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9931718	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9938313	1.00[CHB][hapmap]

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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
5	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
6	esv2755860	chr16:81262516-81333568	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7188650	GAN	cis	parietal	SCAN
rs7188650	PKD1L2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81284600-81324600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:81309200-81345200	Weak transcription	Brain Hippocampus Middle	brain
3	chr16:81311000-81322200	Weak transcription	Esophagus	oesophagus
4	chr16:81312800-81315400	Enhancers	HUVEC	blood vessel
5	chr16:81312800-81319000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:81313000-81315600	Weak transcription	Placenta	Placenta
7	chr16:81314000-81314400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr16:81314000-81315000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:81314000-81315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:81314200-81314600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:81314200-81314800	Enhancers	NH-A	brain

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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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