Variant report

Variant	rs16951534
Chromosome Location	chr16:79882769-79882770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11150223	0.98[AMR][1000 genomes]
rs11641099	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11649129	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16951530	0.81[ASN][1000 genomes]
rs4591156	0.82[AMR][1000 genomes]
rs7184127	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7190136	0.82[ASN][1000 genomes]
rs7191528	0.97[AMR][1000 genomes]
rs7195432	0.82[ASN][1000 genomes]
rs7205082	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7206752	0.84[EUR][1000 genomes]
rs9928685	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1059511	chr16:79847882-79925436	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv542984	chr16:79847882-79925436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv573290	chr16:79853267-79939504	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv573291	chr16:79881386-79931595	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16951534	LQK1	trans	cerebellum	SCAN
rs16951534	TMEM231	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79879600-79885200	Enhancers	Thymus	Thymus
2	chr16:79879800-79884600	Enhancers	Fetal Thymus	thymus
3	chr16:79880000-79883400	Weak transcription	Primary T cells from cord blood	blood
4	chr16:79880600-79884800	Enhancers	NHEK	skin
5	chr16:79880800-79882800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr16:79880800-79883600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr16:79880800-79885200	Enhancers	Colon Smooth Muscle	Colon
8	chr16:79881400-79882800	Weak transcription	Fetal Intestine Large	intestine
9	chr16:79881400-79882800	Weak transcription	Placenta	Placenta
10	chr16:79881400-79883200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:79881600-79883000	Weak transcription	GM12878-XiMat	blood
12	chr16:79881800-79883000	Weak transcription	Gastric	stomach
13	chr16:79882200-79882800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr16:79882200-79883400	Enhancers	Esophagus	oesophagus
15	chr16:79882400-79882800	Enhancers	Fetal Lung	lung
16	chr16:79882400-79882800	Enhancers	Fetal Stomach	stomach
17	chr16:79882600-79882800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:79882600-79883200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr16:79882600-79883200	Enhancers	Placenta Amnion	Placenta Amnion

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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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