Variant report

Variant	rs13407240
Chromosome Location	chr2:149365766-149365767
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:149351334..149352440-chr2:149364775..149365779,24	MCF-7	breast:
2	chr2:149359200..149362082-chr2:149364841..149366905,3	K562	blood:
3	chr2:149351334..149352801-chr2:149364775..149365773,14	MCF-7	breast:
4	chr2:149350840..149353957-chr2:149362704..149366658,3	MCF-7	breast:
5	chr2:149364293..149368189-chr2:149401143..149403866,4	K562	blood:
6	chr2:149364050..149366946-chr2:149371710..149373906,2	MCF-7	breast:
7	chr2:149363805..149366494-chr2:149401169..149403813,2	MCF-7	breast:
8	chr2:149365091..149367494-chr2:149401143..149403866,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135999	Chromatin interaction
ENSG00000232238	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10165986	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10171728	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177983	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10181555	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10181614	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10190474	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10200061	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204718	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10497035	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10928401	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10928402	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10928408	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11687034	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687783	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688979	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12691801	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016446	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13427633	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16828908	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16828910	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2382230	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28533220	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3936439	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4450539	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4624325	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972282	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4972374	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6430322	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6430326	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6716704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736226	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736270	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736369	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6739607	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747262	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6750878	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7574168	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574666	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769079	0.85[ASN][1000 genomes]
rs921242	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921243	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636222	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1827161	chr2:149352353-149475737	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149352800-149365800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149364400-149366000	Enhancers	Placenta	Placenta
3	chr2:149365000-149366000	Enhancers	Hela-S3	cervix
4	chr2:149365600-149366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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