Variant report

Variant	rs3899676
Chromosome Location	chr12:58027916-58027917
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57940164..57942070-chr12:58025601..58028102,2	MCF-7	breast:
2	chr12:58026571..58028240-chr12:58118727..58121626,2	MCF-7	breast:
3	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
4	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:
5	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:
6	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
7	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:
8	chr12:57983391..57985108-chr12:58026747..58028430,2	MCF-7	breast:
9	chr12:58026019..58028946-chr12:58148453..58151531,3	K562	blood:
10	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000175203	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000139266	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11172290	0.87[ASN][1000 genomes]
rs12296706	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12304013	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12318458	0.88[ASN][1000 genomes]
rs12320537	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12322482	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2258877	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2619468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619469	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2619470	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2640607	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34919374	0.85[ASN][1000 genomes]
rs35831868	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71432310	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715930	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774896	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774897	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774898	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774899	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3404611	chr12:58026085-58030983	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
5	esv1797714	chr12:58026786-58028934	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
6	nsv511490	chr12:58026786-58035706	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
7	esv3493503	chr12:58026835-58030383	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
8	esv3493502	chr12:58027226-58031438	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	n/a
9	nsv559037	chr12:58027307-58028863	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
10	esv3493505	chr12:58027335-58030233	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
11	esv2608296	chr12:58027542-58030180	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
12	esv3375578	chr12:58027552-58029787	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
13	esv3493506	chr12:58027852-58029342	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
14	esv2399103	chr12:58027872-58029453	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
15	esv3321651	chr12:58027910-58029372	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58027200-58028000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:58027200-58033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:58027600-58028200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:58027600-58034000	Weak transcription	K562	blood
5	chr12:58027800-58028000	Flanking Active TSS	Hela-S3	cervix
6	chr12:58027800-58030600	Weak transcription	A549	lung

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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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