Variant report

Variant	rs723774
Chromosome Location	chr20:25452150-25452151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs2072975	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072977	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235605	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235606	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235607	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2261177	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2263205	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2294583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2482908	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2482933	0.88[AMR][1000 genomes]
rs2482934	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2482947	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2500395	0.83[AMR][1000 genomes]
rs2500403	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2500441	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2500442	0.82[AMR][1000 genomes]
rs59046052	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6050603	0.85[AMR][1000 genomes]
rs6132842	0.82[AMR][1000 genomes]
rs6132851	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6138569	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6138573	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138576	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138580	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138584	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138595	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138598	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6138599	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138601	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6138604	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6138611	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6138616	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6138622	0.90[AMR][1000 genomes]
rs6138623	0.90[AMR][1000 genomes]
rs6138625	0.84[AMR][1000 genomes]
rs6138631	0.85[AMR][1000 genomes]
rs6138633	0.86[AMR][1000 genomes]
rs878176	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	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
9	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs723774	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs723774	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs723774	PYGB	cis	Whole Blood	GTEx
rs723774	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs723774	PYGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25425600-25453200	Weak transcription	Small Intestine	intestine
2	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
3	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:25429800-25458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
6	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr20:25432600-25452400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
9	chr20:25435600-25459000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr20:25435800-25465600	Weak transcription	NH-A	brain
11	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr20:25437800-25454600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr20:25438000-25452600	Strong transcription	Brain Germinal Matrix	brain
14	chr20:25438000-25456400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr20:25438200-25452400	Strong transcription	Fetal Brain Female	brain
16	chr20:25438400-25452600	Strong transcription	Ovary	ovary
17	chr20:25438400-25455400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:25438600-25453200	Strong transcription	Fetal Intestine Small	intestine
19	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:25438800-25455000	Strong transcription	Fetal Intestine Large	intestine
21	chr20:25438800-25472600	Strong transcription	HepG2	liver
22	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
23	chr20:25441000-25452200	Strong transcription	A549	lung
24	chr20:25441800-25455000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr20:25442200-25460000	Weak transcription	Brain Angular Gyrus	brain
26	chr20:25443200-25459000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr20:25443800-25457400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr20:25444200-25452600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr20:25445200-25452200	Strong transcription	Brain Anterior Caudate	brain
30	chr20:25446000-25459600	Weak transcription	Fetal Brain Male	brain
31	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
32	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr20:25446400-25452400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:25446400-25455200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
36	chr20:25446600-25457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
38	chr20:25448000-25452200	Strong transcription	Pancreas	Pancrea
39	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr20:25448400-25456600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr20:25448400-25458800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:25448400-25459000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr20:25448800-25453600	Weak transcription	Brain Substantia Nigra	brain
45	chr20:25448800-25464600	Weak transcription	HUVEC	blood vessel
46	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr20:25449000-25459000	Weak transcription	Adipose Nuclei	Adipose
48	chr20:25449000-25459400	Weak transcription	Right Ventricle	heart
49	chr20:25449400-25452200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr20:25449400-25459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links