Variant report

Variant	rs4896767
Chromosome Location	chr6:145311090-145311091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1111810	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13216871	0.82[CHB][hapmap]
rs4896766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570667	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6917204	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6937673	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9285506	0.86[ASN][1000 genomes]
rs9322008	0.86[ASN][1000 genomes]
rs9322009	0.84[ASN][1000 genomes]
rs9376879	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9386093	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9390266	0.86[ASN][1000 genomes]
rs9403644	0.82[ASN][1000 genomes]
rs9497163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	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	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886742	chr6:145269757-145376903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4896767	PLAGL1	cis	cerebellum	SCAN
rs4896767	VTA1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145308200-145311800	Weak transcription	Stomach Mucosa	stomach
2	chr6:145310400-145311400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:145310400-145311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:145310800-145311200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:145310800-145311200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:145311000-145314600	Weak transcription	HUVEC	blood vessel
7	chr6:145311000-145315000	Weak transcription	NHDF-Ad	bronchial

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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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