Variant report

Variant	rs3860806
Chromosome Location	chr5:98287008-98287009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:98286978-98287616	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:98286643-98287432	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98286475..98288503-chr5:98329447..98332320,2	MCF-7	breast:
2	chr5:98263888..98266845-chr5:98284652..98287540,3	K562	blood:
3	chr5:98286684..98288719-chrX:40290697..40292204,2	MCF-7	breast:
4	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
5	chr5:98276177..98277799-chr5:98286832..98289590,2	MCF-7	breast:
6	chr5:98286657..98289622-chr5:98293190..98295211,2	K562	blood:
7	chr5:98285322..98288354-chr5:98290192..98292077,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1007453	0.85[AFR][1000 genomes]
rs10515285	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17166461	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17166471	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3777005	1.00[CHB][hapmap]
rs55654090	0.86[AFR][1000 genomes]
rs57249217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57253975	0.90[AFR][1000 genomes]
rs58477983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60298381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61515191	0.90[AFR][1000 genomes]
rs6864720	0.82[AFR][1000 genomes]
rs731496	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73153600	0.82[AFR][1000 genomes]
rs73155434	1.00[AMR][1000 genomes]
rs73155446	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73155478	0.90[AFR][1000 genomes]
rs73155484	0.81[AFR][1000 genomes]
rs73157407	0.86[AFR][1000 genomes]
rs73157426	0.86[AFR][1000 genomes]
rs73776061	0.80[AFR][1000 genomes]
rs7732611	0.90[AFR][1000 genomes]
rs963689	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
2	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
3	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:98279400-98298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:98282600-98290400	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:98283800-98293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:98286200-98288200	Weak transcription	K562	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