Variant report

Variant	rs2424509
Chromosome Location	chr20:23040634-23040635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23036142..23038357-chr20:23040495..23043468,2	K562	blood:
2	chr20:23033798..23035725-chr20:23039013..23041466,2	MCF-7	breast:
3	chr20:23037834..23043617-chr20:23045683..23049258,6	MCF-7	breast:
4	chr20:23039939..23042121-chr20:23116423..23118513,2	K562	blood:
5	chr20:23030229..23033770-chr20:23036359..23041230,6	K562	blood:

Variant related genes	Relation type
ENSG00000178726	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040588	0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821119	0.92[EUR][1000 genomes]
rs1835702	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1835703	0.88[EUR][1000 genomes]
rs1835704	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1998079	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1998080	0.91[EUR][1000 genomes]
rs2007743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019632	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144939	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2207110	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2255937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424503	0.81[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2424510	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424511	0.92[EUR][1000 genomes]
rs2567619	0.93[EUR][1000 genomes]
rs2749813	0.91[EUR][1000 genomes]
rs2749817	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036291	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048519	0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6048526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048533	0.93[EUR][1000 genomes]
rs6076016	0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6082997	0.93[EUR][1000 genomes]
rs6083000	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23032600-23041800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:23032800-23041400	Weak transcription	Spleen	Spleen
3	chr20:23038400-23046600	Enhancers	Fetal Lung	lung
4	chr20:23039600-23043400	Enhancers	Dnd41	blood
5	chr20:23039800-23046000	Enhancers	Fetal Muscle Leg	muscle
6	chr20:23040000-23042400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:23040200-23041400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:23040200-23041600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr20:23040200-23041800	Enhancers	HSMM	muscle
10	chr20:23040200-23042400	Enhancers	Lung	lung
11	chr20:23040200-23043600	Enhancers	Placenta	Placenta
12	chr20:23040200-23043800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:23040200-23043800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr20:23040200-23046800	Enhancers	Fetal Stomach	stomach
15	chr20:23040400-23041000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:23040400-23041200	Enhancers	K562	blood
17	chr20:23040400-23042000	Enhancers	Aorta	Aorta
18	chr20:23040400-23042000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr20:23040400-23043200	Enhancers	Brain Substantia Nigra	brain
20	chr20:23040400-23043400	Enhancers	Adipose Nuclei	Adipose
21	chr20:23040400-23043600	Enhancers	Left Ventricle	heart
22	chr20:23040400-23043600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr20:23040400-23044400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr20:23040400-23044600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:23040400-23044800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr20:23040400-23044800	Enhancers	HUVEC	blood vessel
27	chr20:23040600-23040800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:23040600-23040800	Enhancers	Brain Anterior Caudate	brain
29	chr20:23040600-23040800	Enhancers	Esophagus	oesophagus
30	chr20:23040600-23040800	Flanking Active TSS	Fetal Kidney	kidney
31	chr20:23040600-23040800	Enhancers	Right Ventricle	heart
32	chr20:23040600-23041200	Enhancers	Psoas Muscle	Psoas
33	chr20:23040600-23041800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr20:23040600-23042000	Enhancers	Brain Germinal Matrix	brain
35	chr20:23040600-23042200	Enhancers	Small Intestine	intestine
36	chr20:23040600-23042600	Flanking Active TSS	HSMMtube	muscle
37	chr20:23040600-23043400	Enhancers	Right Atrium	heart
38	chr20:23040600-23043600	Enhancers	Ovary	ovary
39	chr20:23040600-23043600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr20:23040600-23044000	Enhancers	NHDF-Ad	bronchial

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