Variant report

Variant	rs13078960
Chromosome Location	chr3:85807590-85807591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:85801802..85803723-chr3:85806304..85808705,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11721040	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11926524	1.00[CEU][hapmap]
rs12714637	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12714640	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13068138	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13085840	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13098327	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1448612	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1597213	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs17355368	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2122042	0.89[CEU][hapmap]
rs7620339	0.84[CEU][hapmap]
rs7622475	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7640660	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7640855	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9309990	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309991	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9309994	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9309995	1.00[YRI][hapmap]
rs9818122	0.89[CEU][hapmap]
rs9820014	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9826482	1.00[CEU][hapmap]
rs9837525	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9852127	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs9852478	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9852859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9869320	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9873441	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9875880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877300	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1005102	chr3:85729640-85829412	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv460753	chr3:85789007-85820416	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv590911	chr3:85789007-85820416	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85801200-85815000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85805000-85810000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:85807200-85807600	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr3:85807200-85808000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:85807200-85808000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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