Variant report

Variant	rs2569369
Chromosome Location	chr19:39599307-39599308
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39599295..39601915-chr19:39625074..39628012,2	MCF-7	breast:
2	chr19:39595170..39597829-chr19:39598452..39601203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269172	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11882372	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1313617	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2569368	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28606601	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs472265	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs506417	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs516004	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563873	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs565812	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs573875	0.82[YRI][hapmap]
rs62119549	0.89[EUR][1000 genomes]
rs62120479	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120480	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120481	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120482	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62120483	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120484	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120485	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62120486	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120488	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62120489	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62120490	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692346	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692438	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs692461	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs692730	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7253778	0.94[YRI][hapmap]
rs7256505	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256546	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73045449	0.82[EUR][1000 genomes]
rs774913	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs774915	0.92[EUR][1000 genomes]
rs774916	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774917	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774918	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774919	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774920	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39575800-39601200	Weak transcription	HMEC	breast
2	chr19:39590400-39602800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:39596400-39600400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:39597000-39600600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:39597200-39600800	Weak transcription	A549	lung
6	chr19:39597400-39601000	Weak transcription	Brain Angular Gyrus	brain
7	chr19:39597400-39601000	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:39597600-39602600	Weak transcription	Brain Anterior Caudate	brain
9	chr19:39597800-39600800	Weak transcription	Placenta	Placenta
10	chr19:39597800-39601000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:39597800-39601200	Weak transcription	Brain Substantia Nigra	brain
12	chr19:39597800-39603000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:39598000-39600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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