Variant report

Variant	rs28464379
Chromosome Location	chr16:30337186-30337187
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11644392	0.86[EUR][1000 genomes]
rs12922786	0.89[EUR][1000 genomes]
rs2911213	0.91[EUR][1000 genomes]
rs4471699	0.85[EUR][1000 genomes]
rs4788408	0.88[EUR][1000 genomes]
rs7186541	0.88[EUR][1000 genomes]
rs7195216	0.90[EUR][1000 genomes]
rs7404371	0.91[EUR][1000 genomes]
rs8048666	0.86[EUR][1000 genomes]
rs8050176	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061165	chr16:29657389-30363743	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	229 gene(s)	inside rSNPs	diseases
4	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
6	esv1829730	chr16:30192562-30359312	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv1830409	chr16:30198079-30345291	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv12853	chr16:30199661-30346806	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	esv1811407	chr16:30206038-30346558	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1805420	chr16:30254410-30345836	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv978131	chr16:30269117-30347376	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1802585	chr16:30278225-30344810	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3362204	chr16:30336501-30338499	Weak transcription Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28464379	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs28464379	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30286000-30345400	Weak transcription	Fetal Stomach	stomach
2	chr16:30288600-30338400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:30306000-30344800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:30310400-30338600	Weak transcription	Left Ventricle	heart
5	chr16:30320400-30345200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:30324200-30345600	Weak transcription	Thymus	Thymus
7	chr16:30325800-30345800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:30326800-30345800	Weak transcription	Lung	lung
9	chr16:30328200-30341600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:30329200-30345200	Weak transcription	Fetal Intestine Small	intestine
11	chr16:30329600-30345400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr16:30331000-30344800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:30332200-30345200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr16:30336200-30344600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:30336400-30345200	Weak transcription	Fetal Thymus	thymus
16	chr16:30336400-30345400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:30337000-30344000	Weak transcription	GM12878-XiMat	blood
18	chr16:30337000-30345200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr16:30337000-30345200	Weak transcription	Primary T helper 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