Variant report

Variant	rs6138691
Chromosome Location	chr20:25840217-25840218
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2275800	0.81[AFR][1000 genomes]
rs34122971	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34249314	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35189947	0.80[EUR][1000 genomes]
rs35822564	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050940	0.90[ASN][1000 genomes]
rs6050943	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050944	0.82[ASN][1000 genomes]
rs6050945	0.86[ASN][1000 genomes]
rs61117562	0.82[EUR][1000 genomes]
rs6115344	0.86[ASN][1000 genomes]
rs6138689	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67051989	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	esv10664	chr20:25767042-25849064	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	esv3502991	chr20:25837879-25847973	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv3502992	chr20:25837879-25847973	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	esv3429566	chr20:25838143-25848095	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6138691	PYGB	cis	Whole Blood	GTEx
rs6138691	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25838400-25840400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr20:25838400-25842000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr20:25838400-25842200	ZNF genes & repeats	Dnd41	blood
4	chr20:25838600-25842000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr20:25839000-25840600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr20:25839200-25840400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr20:25839200-25842000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr20:25839400-25840400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:25839400-25840400	Weak transcription	Ovary	ovary
10	chr20:25839400-25840400	Weak transcription	Psoas Muscle	Psoas
11	chr20:25839400-25840400	Weak transcription	Right Atrium	heart
12	chr20:25839400-25840400	Weak transcription	A549	lung
13	chr20:25839400-25841000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:25839400-25841400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:25839400-25842000	Bivalent Enhancer	Placenta	Placenta
16	chr20:25839400-25842600	Enhancers	Fetal Heart	heart
17	chr20:25839600-25840400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr20:25839600-25840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:25839600-25840400	Bivalent Enhancer	Adipose Nuclei	Adipose
20	chr20:25839600-25840400	Weak transcription	Gastric	stomach
21	chr20:25839600-25840400	Weak transcription	Spleen	Spleen
22	chr20:25840000-25840400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr20:25840000-25840400	Enhancers	Liver	Liver
24	chr20:25840000-25840400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
25	chr20:25840000-25840400	Enhancers	GM12878-XiMat	blood
26	chr20:25840000-25840400	Enhancers	K562	blood
27	chr20:25840000-25840600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:25840000-25840800	Active TSS	Brain Anterior Caudate	brain
29	chr20:25840000-25841200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
30	chr20:25840000-25841200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr20:25840000-25841600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr20:25840000-25842000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr20:25840000-25842000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
34	chr20:25840000-25845000	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr20:25840200-25840400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:25840200-25840400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr20:25840200-25840400	Bivalent Enhancer	Primary T cells from cord blood	blood
38	chr20:25840200-25840400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr20:25840200-25840400	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr20:25840200-25840400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:25840200-25840400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr20:25840200-25840400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr20:25840200-25840400	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr20:25840200-25840400	Flanking Active TSS	Fetal Brain Female	brain
45	chr20:25840200-25840400	Enhancers	Left Ventricle	heart
46	chr20:25840200-25840400	Enhancers	Pancreas	Pancrea
47	chr20:25840200-25840400	Bivalent/Poised TSS	NHEK	skin
48	chr20:25840200-25840600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
49	chr20:25840200-25840600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:25840200-25840600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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