Variant report

Variant	rs3752273
Chromosome Location	chr20:25594783-25594784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25591410..25597359-chr20:25600309..25606040,12	K562	blood:
2	chr20:25589936..25592096-chr20:25592501..25595194,2	MCF-7	breast:
3	chr20:25593129..25595979-chr20:25604532..25607057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251883	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13040726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987764	1.00[CHB][hapmap]
rs1983974	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2387976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2387977	0.85[CEU][hapmap]
rs34485039	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374701	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs376742	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs390123	0.89[ASN][1000 genomes]
rs400357	0.89[ASN][1000 genomes]
rs404775	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs405822	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs409853	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4423675	1.00[YRI][hapmap]
rs443009	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4815429	0.89[ASN][1000 genomes]
rs4815431	0.89[ASN][1000 genomes]
rs4815437	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037158	1.00[CHB][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6050679	0.89[ASN][1000 genomes]
rs6076358	0.89[ASN][1000 genomes]
rs6076364	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076366	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076369	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083851	0.89[ASN][1000 genomes]
rs6083860	0.89[ASN][1000 genomes]
rs6083891	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107062	1.00[CHB][hapmap]
rs6107064	1.00[CHB][hapmap]
rs6115188	0.89[ASN][1000 genomes]
rs6115190	1.00[CHB][hapmap]
rs6115210	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6138593	0.89[ASN][1000 genomes]
rs7268237	1.00[CHB][hapmap]
rs958075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3752273	ABHD12	cis	Frontal Cortex	GTEx
rs3752273	ABHD12	cis	Cerebellum	GTEx
rs3752273	ABHD12	cis	Temporal Cortex	GTEx
rs3752273	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs3752273	ABHD12	cis	uninvolved skin	skin_eQTL
rs3752273	NINL	cis	Thyroid	GTEx
rs3752273	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs3752273	ABHD12	cis	Brain Pons	GTEx
rs3752273	ABHD12	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
2	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:25582000-25594800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr20:25582000-25602800	Weak transcription	Osteobl	bone
5	chr20:25585600-25595200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:25586000-25602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr20:25586200-25602800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr20:25587000-25603000	Weak transcription	HSMMtube	muscle
9	chr20:25587400-25600400	Weak transcription	K562	blood
10	chr20:25587600-25601400	Weak transcription	Pancreas	Pancrea
11	chr20:25588000-25595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr20:25588400-25597800	Strong transcription	Dnd41	blood
13	chr20:25588400-25599200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr20:25588600-25596200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr20:25588600-25599400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr20:25588600-25599400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr20:25588600-25602800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr20:25588800-25595800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:25589200-25601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:25589200-25602600	Weak transcription	Right Ventricle	heart
21	chr20:25590800-25595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:25590800-25602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr20:25590800-25603200	Weak transcription	Fetal Intestine Large	intestine
24	chr20:25591000-25595400	Weak transcription	Lung	lung
25	chr20:25591000-25603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:25591200-25595400	Weak transcription	Gastric	stomach
27	chr20:25591400-25602800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr20:25591600-25595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:25591600-25600200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr20:25591600-25602800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr20:25591600-25603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr20:25591600-25603200	Weak transcription	Fetal Lung	lung
33	chr20:25592000-25595400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:25592000-25595800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr20:25592200-25597200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr20:25592200-25602600	Weak transcription	Colon Smooth Muscle	Colon
37	chr20:25592200-25602600	Weak transcription	NHLF	lung
38	chr20:25592200-25602800	Weak transcription	Small Intestine	intestine
39	chr20:25592200-25602800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr20:25592200-25603200	Weak transcription	Brain Germinal Matrix	brain
41	chr20:25592600-25597600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:25592600-25602800	Weak transcription	Esophagus	oesophagus
43	chr20:25592600-25603200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr20:25592800-25603200	Weak transcription	Fetal Kidney	kidney
45	chr20:25592800-25603200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr20:25593000-25595200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr20:25593000-25596400	Weak transcription	NHEK	skin
48	chr20:25593000-25597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr20:25593000-25597000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:25593000-25597000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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