Variant report

Variant	rs4280527
Chromosome Location	chr20:25544014-25544015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1047171	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11087520	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11087521	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11699203	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12428	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13038834	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1541061	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1883528	0.80[ASN][1000 genomes]
rs1983974	0.82[CEU][hapmap]
rs1985737	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2104734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2151144	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2179459	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2184000	0.80[EUR][1000 genomes]
rs2263204	0.81[EUR][1000 genomes]
rs2387881	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2387885	0.86[EUR][1000 genomes]
rs2387887	0.83[EUR][1000 genomes]
rs2387891	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2424712	0.83[EUR][1000 genomes]
rs2424713	0.84[EUR][1000 genomes]
rs2424714	0.83[EUR][1000 genomes]
rs2424715	0.82[EUR][1000 genomes]
rs2424716	0.86[EUR][1000 genomes]
rs2482911	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2482913	0.83[EUR][1000 genomes]
rs2482918	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2482943	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2500399	0.96[CEU][hapmap]
rs2500405	0.96[CEU][hapmap]
rs2500417	0.82[EUR][1000 genomes]
rs2500418	0.82[EUR][1000 genomes]
rs2500424	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2500436	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2500448	0.83[EUR][1000 genomes]
rs2856	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2892408	0.80[ASN][1000 genomes]
rs372678	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs374701	0.82[CEU][hapmap]
rs3761117	0.92[CEU][hapmap]
rs376742	0.82[CEU][hapmap]
rs397119	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs398036	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs401166	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs404394	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs404775	0.82[CEU][hapmap]
rs405822	0.83[CEU][hapmap]
rs408853	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs409853	0.83[CEU][hapmap]
rs416745	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs417110	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs417130	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs422424	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs422844	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs424487	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs431579	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs433352	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs437635	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs442834	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs443009	0.82[CEU][hapmap]
rs446649	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs447722	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs448396	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs449370	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs449703	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs453329	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs454723	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4813562	0.92[CEU][hapmap]
rs4815411	0.92[CEU][hapmap]
rs4815412	0.92[CEU][hapmap]
rs4815417	0.92[CEU][hapmap]
rs4815424	0.83[EUR][1000 genomes]
rs4815426	0.80[EUR][1000 genomes]
rs4815436	0.80[ASN][1000 genomes]
rs6037097	0.92[CEU][hapmap]
rs6037103	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6037105	0.92[CEU][hapmap]
rs6037120	0.86[EUR][1000 genomes]
rs6037121	0.83[EUR][1000 genomes]
rs6037125	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6037126	0.88[EUR][1000 genomes]
rs6037169	0.83[ASN][1000 genomes]
rs6050565	0.92[CEU][hapmap]
rs6050567	0.92[CEU][hapmap]
rs6050573	0.92[CEU][hapmap]
rs6050598	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6050599	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6050602	0.80[EUR][1000 genomes]
rs6050609	0.82[EUR][1000 genomes]
rs6050611	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6050617	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs6050626	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6050629	0.82[EUR][1000 genomes]
rs6050630	0.83[EUR][1000 genomes]
rs6050631	0.86[EUR][1000 genomes]
rs6050632	0.83[EUR][1000 genomes]
rs6050679	0.85[CEU][hapmap]
rs6083818	0.92[CEU][hapmap]
rs6083828	0.92[CEU][hapmap]
rs6083845	0.82[CEU][hapmap]
rs6083853	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6083855	0.80[EUR][1000 genomes]
rs6083856	0.83[EUR][1000 genomes]
rs6083862	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6107031	0.92[CEU][hapmap]
rs6107044	0.83[EUR][1000 genomes]
rs6107045	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6107046	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6107047	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6107052	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115159	0.92[CEU][hapmap]
rs6115182	0.82[EUR][1000 genomes]
rs6115183	0.82[EUR][1000 genomes]
rs6115185	0.83[EUR][1000 genomes]
rs6115191	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115200	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6115204	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6115214	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115215	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115220	0.80[ASN][1000 genomes]
rs6115229	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6115232	0.83[ASN][1000 genomes]
rs6132833	0.86[EUR][1000 genomes]
rs6132835	0.84[EUR][1000 genomes]
rs6132845	0.80[EUR][1000 genomes]
rs6132848	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132850	0.80[ASN][1000 genomes]
rs6138571	0.85[EUR][1000 genomes]
rs6138572	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138575	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138588	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6138600	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6138609	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6515651	0.86[EUR][1000 genomes]
rs7270835	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs761025	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs8113919	0.83[EUR][1000 genomes]
rs84816	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs928121	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
17	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
18	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4280527	ABHD12	cis	multi-tissue	Pritchard
rs4280527	ABHD12	cis	Cerebellum	GTEx
rs4280527	NINL	cis	Thyroid	GTEx
rs4280527	PYGB	cis	Whole Blood	GTEx
rs4280527	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs4280527	C20orf22	cis	multi-tissue	Pritchard
rs4280527	PYGB	cis	multi-tissue	Pritchard
rs4280527	ABHD12	cis	Brain Pons	GTEx
rs4280527	ABHD12	cis	Frontal Cortex	GTEx
rs4280527	ABHD12	cis	lesional skin	skin_eQTL
rs4280527	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs4280527	ABHD12	cis	uninvolved skin	skin_eQTL
rs4280527	ABHD12	cis	Temporal Cortex	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
3	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:25531000-25554000	Weak transcription	Osteobl	bone
5	chr20:25531200-25544400	Weak transcription	Fetal Brain Male	brain
6	chr20:25531200-25559600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:25532600-25551600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr20:25532600-25559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
10	chr20:25532800-25544400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr20:25533400-25544200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr20:25533400-25546000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr20:25533400-25549600	Weak transcription	Fetal Intestine Small	intestine
14	chr20:25534800-25550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:25534800-25551800	Weak transcription	HUVEC	blood vessel
16	chr20:25534800-25557600	Weak transcription	Pancreas	Pancrea
17	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
18	chr20:25535000-25545400	Weak transcription	Thymus	Thymus
19	chr20:25535000-25546400	Weak transcription	Ovary	ovary
20	chr20:25535000-25550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr20:25535000-25550200	Weak transcription	Gastric	stomach
22	chr20:25535000-25554400	Weak transcription	Brain Anterior Caudate	brain
23	chr20:25535000-25560000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr20:25535200-25546000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
27	chr20:25540400-25545600	Weak transcription	Fetal Heart	heart
28	chr20:25540800-25544400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr20:25540800-25549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:25540800-25552600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr20:25541200-25549400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25541200-25550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:25541400-25544600	Weak transcription	Fetal Stomach	stomach
34	chr20:25541600-25544400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr20:25541600-25546200	Weak transcription	A549	lung
36	chr20:25541800-25544400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr20:25541800-25546400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr20:25543200-25545000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr20:25543400-25544800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr20:25543400-25544800	ZNF genes & repeats	Dnd41	blood
41	chr20:25543600-25544800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr20:25543800-25544200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
43	chr20:25543800-25544400	Weak transcription	HepG2	liver
44	chr20:25543800-25544600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr20:25543800-25544800	ZNF genes & repeats	Fetal Lung	lung
46	chr20:25543800-25545200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25544000-25544600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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