Variant report

Variant	rs3844442
Chromosome Location	chr19:41415112-41415113
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10411264	0.81[JPT][hapmap]
rs10419393	0.81[JPT][hapmap]
rs10419589	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10424844	0.95[ASN][1000 genomes]
rs10426903	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083584	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3852870	0.81[JPT][hapmap]
rs3869579	0.81[JPT][hapmap]
rs3875159	0.81[JPT][hapmap]
rs4105141	0.85[JPT][hapmap]
rs4803393	0.81[JPT][hapmap]
rs4803400	0.81[JPT][hapmap]
rs5007415	0.81[JPT][hapmap]
rs6508953	0.81[JPT][hapmap]
rs7252852	0.81[JPT][hapmap]
rs7252878	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8108939	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv3337314	chr19:41388910-41534583	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv437830	chr19:41408746-41515702	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3844442	FBXO46	cis	parietal	SCAN
rs3844442	SLC17A7	cis	parietal	SCAN
rs3844442	NANOS2	cis	parietal	SCAN
rs3844442	PTH2	cis	parietal	SCAN
rs3844442	PRKD2	cis	parietal	SCAN
rs3844442	ZNF229	cis	parietal	SCAN
rs3844442	LIG1	cis	cerebellum	SCAN
rs3844442	QPCTL	cis	parietal	SCAN
rs3844442	SNORD35A	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41413600-41415400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:41413800-41415200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr19:41414400-41415200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr19:41414400-41415400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:41414600-41415400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:41414600-41415400	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:41414600-41415400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr19:41414600-41415400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:41414600-41415600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr19:41414600-41415600	Bivalent Enhancer	A549	lung
11	chr19:41414800-41415200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr19:41414800-41415200	Enhancers	Adipose Nuclei	Adipose
13	chr19:41414800-41419400	Weak transcription	Pancreas	Pancrea
14	chr19:41415000-41415200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr19:41415000-41415200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:41415000-41415200	Enhancers	K562	blood
17	chr19:41415000-41415400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:41415000-41415400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr19:41415000-41415400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

Quick Search:

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

what's new

Quick links