Variant report

Variant	rs2446999
Chromosome Location	chr12:49274072-49274073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
2	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
3	chr12:49273861..49275618-chr12:49278332..49280043,2	MCF-7	breast:
4	chr12:49244448..49248825-chr12:49273797..49278851,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10783287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875883	0.82[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875885	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs11168773	0.94[ASN][1000 genomes]
rs12369505	0.85[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2293449	0.80[CEU][hapmap]
rs2446984	0.80[AMR][1000 genomes]
rs2446985	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2446986	0.90[ASN][1000 genomes]
rs2446987	0.92[ASN][1000 genomes]
rs2447000	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2447001	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2453476	0.91[ASN][1000 genomes]
rs2926806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934998	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958875	0.92[ASN][1000 genomes]
rs4760647	0.96[ASN][1000 genomes]
rs833476	0.93[ASN][1000 genomes]
rs833478	0.92[ASN][1000 genomes]
rs833479	0.92[ASN][1000 genomes]
rs833483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833839	0.92[CEU][hapmap]
rs833841	0.92[CEU][hapmap]

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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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 target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2446999	CCDC65	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49271400-49275000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:49271400-49278200	Enhancers	Liver	Liver
3	chr12:49272800-49275200	Weak transcription	Fetal Intestine Large	intestine
4	chr12:49272800-49275200	Weak transcription	Fetal Intestine Small	intestine
5	chr12:49273800-49274400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:49273800-49274800	Bivalent Enhancer	HepG2	liver
7	chr12:49273800-49276800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:49274000-49274400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
9	chr12:49274000-49274600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:49274000-49275600	Enhancers	A549	lung
11	chr12:49274000-49278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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