Variant report

Variant	rs13166976
Chromosome Location	chr5:179898700-179898701
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179715141..179717166-chr5:179896710..179898786,2	MCF-7	breast:
2	chr5:179717189..179723869-chr5:179893101..179900893,11	MCF-7	breast:
3	chr5:179890863..179893411-chr5:179896364..179898839,3	K562	blood:
4	chr5:179897206..179899731-chr5:179901883..179904757,4	K562	blood:
5	chr5:179769448..179771276-chr5:179896602..179898870,2	MCF-7	breast:
6	chr5:179720128..179721419-chr5:179897501..179899069,16	MCF-7	breast:
7	chr5:179718174..179720847-chr5:179898001..179899613,2	MCF-7	breast:
8	chr5:179739299..179743379-chr5:179893176..179898905,6	MCF-7	breast:
9	chr5:179720229..179721221-chr5:179897697..179898870,4	K562	blood:
10	chr5:179738783..179741691-chr5:179897243..179899588,2	MCF-7	breast:
11	chr5:179896623..179899135-chr5:179900474..179902036,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11740624	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743486	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs11744788	0.84[ASN][1000 genomes]
rs11745221	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745985	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13158291	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13158411	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13163282	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13164626	0.83[ASN][1000 genomes]
rs13167409	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13172461	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13176745	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178900	0.85[EUR][1000 genomes]
rs55704211	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405490	0.81[EUR][1000 genomes]
rs67466093	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs872365	0.81[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13166976	BTNL3	cis	cerebellum	SCAN
rs13166976	BTNL3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179895000-179912200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:179897600-179899200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr5:179897600-179900000	Genic enhancers	A549	lung
4	chr5:179898200-179899000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:179898200-179899200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr5:179898200-179900200	Enhancers	Adipose Nuclei	Adipose
7	chr5:179898400-179899000	Weak transcription	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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