Variant report

Variant	rs2409105
Chromosome Location	chr13:55167935-55167936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:55165909..55168648-chr13:55172019..55174969,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1020967	0.88[EUR][1000 genomes]
rs11840450	0.81[EUR][1000 genomes]
rs1382461	0.99[EUR][1000 genomes]
rs1478653	0.81[EUR][1000 genomes]
rs2153713	0.81[EUR][1000 genomes]
rs2185642	0.97[EUR][1000 genomes]
rs2447970	0.87[EUR][1000 genomes]
rs2491038	0.88[EUR][1000 genomes]
rs2491039	0.87[EUR][1000 genomes]
rs2898093	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56230005	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318471	0.99[EUR][1000 genomes]
rs7323791	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994187	0.98[EUR][1000 genomes]
rs7997596	0.81[EUR][1000 genomes]
rs9527228	0.81[EUR][1000 genomes]
rs9527231	0.99[EUR][1000 genomes]
rs9536767	0.97[EUR][1000 genomes]
rs9536768	0.98[EUR][1000 genomes]
rs9536769	0.98[EUR][1000 genomes]
rs9536772	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536774	0.97[EUR][1000 genomes]
rs9536775	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv917186	chr13:55022134-55433232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv561702	chr13:55086271-55808127	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1043044	chr13:55102831-55285581	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1048599	chr13:55143426-55476042	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1051640	chr13:55143426-55478547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv561703	chr13:55143754-55473732	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv916104	chr13:55154006-55433232	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1052745	chr13:55159674-55459161	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv541779	chr13:55159674-55459161	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:55161000-55173200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr13:55161200-55168200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:55161200-55171200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:55161200-55171400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:55166800-55168000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr13:55167200-55168000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:55167200-55168000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:55167400-55168000	ZNF genes & repeats	Pancreas	Pancrea
9	chr13:55167400-55169800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:55167600-55168200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

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