Variant report

Variant	rs998084
Chromosome Location	chr9:93340595-93340596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10993593	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993603	0.94[ASN][1000 genomes]
rs10993606	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10993610	0.82[ASN][1000 genomes]
rs12378398	1.00[ASN][1000 genomes]
rs1331501	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs1473412	0.82[ASN][1000 genomes]
rs4323593	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62556816	0.82[ASN][1000 genomes]
rs7028171	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs7036896	0.88[ASN][1000 genomes]
rs72744795	0.94[ASN][1000 genomes]
rs7847229	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7871670	0.82[ASN][1000 genomes]
rs7872323	0.94[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	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893566	chr9:93209923-93439259	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs998084	NXNL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93339600-93346000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:93340000-93340600	Enhancers	Placenta	Placenta
3	chr9:93340200-93340800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:93340200-93341000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:93340200-93341000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:93340400-93340800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:93340400-93341000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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