Variant report

Variant	rs56238023
Chromosome Location	chr20:25516947-25516948
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	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11699872	0.94[ASN][1000 genomes]
rs12480853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1888037	0.82[ASN][1000 genomes]
rs55792313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6107050	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6115202	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6115227	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73109499	0.83[ASN][1000 genomes]
rs73597824	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9305141	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56238023	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs56238023	PYGB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:25498200-25519400	Weak transcription	Gastric	stomach
4	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
7	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:25507400-25518400	Weak transcription	A549	lung
9	chr20:25507600-25518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
11	chr20:25511200-25517600	Weak transcription	Fetal Brain Female	brain
12	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
13	chr20:25513200-25517400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:25513400-25517000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr20:25513400-25517000	Enhancers	Fetal Lung	lung
16	chr20:25513400-25519200	Enhancers	Liver	Liver
17	chr20:25513600-25518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:25513600-25518600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr20:25513600-25519400	Weak transcription	Esophagus	oesophagus
20	chr20:25513800-25520400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:25513800-25521200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr20:25514000-25517600	Weak transcription	Dnd41	blood
23	chr20:25514200-25517000	Enhancers	Brain Anterior Caudate	brain
24	chr20:25514200-25517800	Enhancers	Brain Substantia Nigra	brain
25	chr20:25514200-25521000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr20:25514400-25517200	Enhancers	Brain Hippocampus Middle	brain
27	chr20:25514400-25520000	Weak transcription	NHLF	lung
28	chr20:25514400-25520800	Weak transcription	Fetal Kidney	kidney
29	chr20:25514400-25522400	Weak transcription	NH-A	brain
30	chr20:25514800-25518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr20:25514800-25519200	Weak transcription	Right Atrium	heart
32	chr20:25514800-25520000	Weak transcription	Osteobl	bone
33	chr20:25514800-25520400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr20:25515000-25519000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr20:25515000-25519600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr20:25515000-25520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:25515000-25520200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25515200-25517000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:25515200-25517600	Weak transcription	Fetal Stomach	stomach
40	chr20:25515200-25518000	Weak transcription	Fetal Intestine Small	intestine
41	chr20:25515200-25518600	Weak transcription	Right Ventricle	heart
42	chr20:25515200-25519200	Weak transcription	Pancreas	Pancrea
43	chr20:25515400-25518200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr20:25515400-25519200	Weak transcription	Colon Smooth Muscle	Colon
45	chr20:25515400-25519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr20:25515400-25520600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr20:25515600-25517600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:25515600-25519600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:25515600-25519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr20:25515600-25520200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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