Variant report

Variant	rs2096281
Chromosome Location	chr20:25849504-25849505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2386786	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs35189947	0.96[ASN][1000 genomes]
rs3949256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050930	0.81[AFR][1000 genomes]
rs6050944	0.83[AMR][1000 genomes]
rs6050945	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6050976	0.82[ASN][1000 genomes]
rs6050978	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61117562	0.96[ASN][1000 genomes]
rs6115344	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6138716	0.93[ASN][1000 genomes]
rs6138728	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs67051989	0.96[ASN][1000 genomes]
rs7272868	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
2	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv979422	chr20:25732656-25867609	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv585749	chr20:25767347-25856929	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv585752	chr20:25786189-25864851	ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv585753	chr20:25786189-25892571	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv585754	chr20:25786301-25864851	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv585755	chr20:25786301-25871801	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv585756	chr20:25786301-25948094	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv585757	chr20:25786301-25948327	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv585758	chr20:25786984-25951658	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv585759	chr20:25787096-25948327	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1059041	chr20:25832105-26007269	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1060065	chr20:25832105-26305567	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
16	nsv9795	chr20:25832369-25851689	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv979451	chr20:25836169-25856112	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2096281	PYGB	cis	Whole Blood	GTEx
rs2096281	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs2096281	CTD-2514C3.1	cis	Artery Tibial	GTEx
rs2096281	FAM182B	cis	Esophagus Muscularis	GTEx
rs2096281	FAM182A,FAM182B	cis	occipital cortex	BrainEAC
rs2096281	FAM182A,FAM182B	cis	hippocampus	BrainEAC
rs2096281	FAM182A,FAM182B	cis	brain	BrainEAC
rs2096281	FAM182A,FAM182B	cis	cerebellar cortex	BrainEAC

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25844800-25849800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr20:25846000-25850000	Active TSS	Brain Anterior Caudate	brain
3	chr20:25848200-25850000	Enhancers	Spleen	Spleen
4	chr20:25848400-25849600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr20:25848400-25849600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:25848400-25849600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
7	chr20:25848400-25849600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr20:25848400-25849600	Active TSS	Brain Angular Gyrus	brain
9	chr20:25848400-25849800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
10	chr20:25848400-25849800	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr20:25848600-25849600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr20:25848600-25849600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr20:25848600-25849600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr20:25848600-25849600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:25848600-25849600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr20:25848600-25849600	Flanking Active TSS	Pancreas	Pancrea
17	chr20:25848600-25849600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
18	chr20:25848600-25849600	Bivalent/Poised TSS	NHDF-Ad	bronchial
19	chr20:25848600-25849600	Bivalent/Poised TSS	Osteobl	bone
20	chr20:25848600-25849800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr20:25848800-25849600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr20:25848800-25849600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr20:25848800-25849600	Active TSS	Right Ventricle	heart
24	chr20:25849000-25849600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr20:25849000-25849600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr20:25849000-25849600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr20:25849000-25849600	Flanking Active TSS	Fetal Brain Male	brain
28	chr20:25849000-25849600	Flanking Active TSS	Fetal Brain Female	brain
29	chr20:25849000-25850000	Weak transcription	Lung	lung
30	chr20:25849200-25849600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr20:25849200-25849600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr20:25849200-25849600	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr20:25849200-25849600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr20:25849200-25849600	Active TSS	Gastric	stomach
35	chr20:25849200-25849800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr20:25849400-25849600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:25849400-25849600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr20:25849400-25849600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr20:25849400-25849600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr20:25849400-25849600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr20:25849400-25849600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
42	chr20:25849400-25849600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr20:25849400-25849600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr20:25849400-25849600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:25849400-25849600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr20:25849400-25849600	Bivalent Enhancer	Placenta	Placenta
47	chr20:25849400-25849600	Bivalent Enhancer	Fetal Stomach	stomach
48	chr20:25849400-25849600	Enhancers	Rectal Smooth Muscle	rectum
49	chr20:25849400-25849600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
50	chr20:25849400-25849800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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