Variant report

Variant	rs2019996
Chromosome Location	chr1:46792060-46792061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10489769	0.81[EUR][1000 genomes]
rs12091789	0.88[EUR][1000 genomes]
rs12137934	0.80[EUR][1000 genomes]
rs12142240	0.84[EUR][1000 genomes]
rs12146051	0.83[EUR][1000 genomes]
rs1475389	0.80[AMR][1000 genomes]
rs17361749	0.81[EUR][1000 genomes]
rs28578741	0.80[AMR][1000 genomes]
rs41293273	0.81[EUR][1000 genomes]
rs41293275	0.81[EUR][1000 genomes]
rs41293277	0.81[EUR][1000 genomes]
rs4313342	0.87[EUR][1000 genomes]
rs6683523	0.88[EUR][1000 genomes]
rs66972124	0.80[EUR][1000 genomes]
rs6697623	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67545510	0.82[EUR][1000 genomes]
rs68083747	0.80[EUR][1000 genomes]
rs72886905	0.80[AMR][1000 genomes]
rs7520482	0.80[AMR][1000 genomes]

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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv947254	chr1:46769363-46808918	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2019996	FAAH	cis	Whole Blood	GTEx
rs2019996	NSUN4	cis	Muscle Skeletal	GTEx
rs2019996	NSUN4	cis	Whole Blood	GTEx
rs2019996	RP5-1109J22.1	cis	Thyroid	GTEx
rs2019996	FAAH	cis	Esophagus Muscularis	GTEx
rs2019996	NSUN4	Cis_1M	lymphoblastoid	RTeQTL
rs2019996	FAAH	cis	Esophagus Mucosa	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46773400-46805400	Weak transcription	Right Atrium	heart
2	chr1:46777400-46799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46781800-46805400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:46783400-46799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:46783600-46797400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:46784000-46799400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:46784000-46805000	Weak transcription	Thymus	Thymus
8	chr1:46786000-46796800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:46787000-46793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:46787200-46794600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:46787400-46793800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:46790800-46792600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr1:46791200-46792200	Active TSS	GM12878-XiMat	blood

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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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