Variant report

Variant	rs56243008
Chromosome Location	chr20:25493065-25493066
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25487968..25491385-chr20:25492316..25494168,3	MCF-7	breast:
2	chr20:25491958..25494931-chr20:25496004..25498993,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11905437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16987806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17244452	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56059261	0.94[EUR][1000 genomes]
rs56251619	0.94[EUR][1000 genomes]
rs6107039	0.94[EUR][1000 genomes]
rs6107049	0.92[EUR][1000 genomes]
rs6115177	0.94[EUR][1000 genomes]
rs6115178	0.94[EUR][1000 genomes]
rs6115187	0.94[EUR][1000 genomes]
rs6115193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115208	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6115211	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115223	0.85[EUR][1000 genomes]
rs7272126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73107474	0.94[EUR][1000 genomes]
rs73111242	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73113144	0.81[AFR][1000 genomes];0.85[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	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56243008	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
2	chr20:25473400-25494400	Strong transcription	Fetal Brain Female	brain
3	chr20:25473600-25494600	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:25473600-25494600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:25473800-25494200	Strong transcription	Thymus	Thymus
6	chr20:25474400-25495200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:25474600-25494800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:25474800-25493400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:25475400-25494000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:25475400-25498000	Weak transcription	Right Ventricle	heart
11	chr20:25477000-25494800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr20:25477400-25495200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr20:25478200-25494800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr20:25478800-25494600	Strong transcription	Fetal Muscle Leg	muscle
15	chr20:25480400-25494600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:25480800-25494600	Strong transcription	Fetal Lung	lung
17	chr20:25481200-25494000	Strong transcription	Dnd41	blood
18	chr20:25481400-25494800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:25482600-25494600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr20:25483000-25494400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:25483000-25494800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr20:25483400-25494600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr20:25485800-25494800	Strong transcription	Fetal Stomach	stomach
24	chr20:25485800-25498600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr20:25487200-25495000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:25487200-25498200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr20:25488000-25494200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:25488000-25495200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:25488200-25496800	Weak transcription	Fetal Heart	heart
30	chr20:25489000-25494400	Strong transcription	Esophagus	oesophagus
31	chr20:25489400-25493200	Strong transcription	Colon Smooth Muscle	Colon
32	chr20:25489400-25493400	Strong transcription	Gastric	stomach
33	chr20:25489400-25493800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr20:25489400-25494200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr20:25489400-25494400	Strong transcription	Adipose Nuclei	Adipose
36	chr20:25489400-25495200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25489400-25495400	Weak transcription	Colonic Mucosa	Colon
38	chr20:25489400-25505800	Weak transcription	NHDF-Ad	bronchial
39	chr20:25489600-25493600	Strong transcription	Brain Anterior Caudate	brain
40	chr20:25489600-25493800	Weak transcription	HSMM	muscle
41	chr20:25489600-25493800	Strong transcription	HSMMtube	muscle
42	chr20:25489600-25494400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:25489600-25494400	Strong transcription	Fetal Intestine Large	intestine
44	chr20:25489600-25494800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr20:25489600-25494800	Strong transcription	Ovary	ovary
46	chr20:25489800-25495000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr20:25489800-25495000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr20:25490000-25493600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:25490000-25494600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr20:25490000-25494800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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