Variant report

Variant	rs1364287
Chromosome Location	chr16:82119100-82119101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10514523	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119933	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11645641	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11645754	1.00[CHB][hapmap]
rs1559428	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981878	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981879	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2955162	0.90[CHB][hapmap]
rs62046326	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046327	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7196807	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723012	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723013	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8191243	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8191248	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs996751	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058368	chr16:82029516-82152788	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv532598	chr16:82034475-82738733	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1061709	chr16:82093183-82159867	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	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
rs1364287	NECAB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82104800-82124400	Weak transcription	Fetal Stomach	stomach
2	chr16:82114800-82119400	Enhancers	Stomach Mucosa	stomach
3	chr16:82115800-82119200	Enhancers	Fetal Intestine Small	intestine
4	chr16:82115800-82119400	Enhancers	Fetal Intestine Large	intestine
5	chr16:82116000-82127400	Weak transcription	Gastric	stomach
6	chr16:82116400-82119200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr16:82117200-82124600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:82117400-82121600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr16:82117800-82119400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr16:82117800-82122800	Enhancers	Liver	Liver
11	chr16:82117800-82124000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:82118000-82119200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr16:82118000-82119600	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr16:82118000-82120000	Weak transcription	Placenta	Placenta
15	chr16:82118000-82135800	Weak transcription	Pancreas	Pancrea
16	chr16:82118400-82119200	Enhancers	HSMMtube	muscle
17	chr16:82118600-82134800	Weak transcription	Colonic Mucosa	Colon
18	chr16:82119000-82119400	Enhancers	NHEK	skin
19	chr16:82119000-82123400	Weak transcription	HepG2	liver

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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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