Variant report

Variant	rs6138623
Chromosome Location	chr20:25617504-25617505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25603901..25606478-chr20:25617196..25618915,2	K562	blood:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs2072975	0.86[AMR][1000 genomes]
rs2072977	0.90[AMR][1000 genomes]
rs2235605	0.90[AMR][1000 genomes]
rs2235606	0.88[AMR][1000 genomes]
rs2235607	0.90[AMR][1000 genomes]
rs2294583	0.90[AMR][1000 genomes]
rs35016365	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35364051	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35672749	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59046052	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050690	0.85[ASN][1000 genomes]
rs6115218	0.91[ASN][1000 genomes]
rs6115241	0.90[ASN][1000 genomes]
rs6132842	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132851	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132857	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6132858	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6132861	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132863	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132864	0.83[EUR][1000 genomes]
rs6138569	0.88[AMR][1000 genomes]
rs6138573	0.90[AMR][1000 genomes]
rs6138576	0.87[AMR][1000 genomes]
rs6138580	0.88[AMR][1000 genomes]
rs6138584	0.88[AMR][1000 genomes]
rs6138595	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138598	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138599	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138601	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138604	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138611	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138625	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138631	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138633	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138639	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138643	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138647	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138650	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138651	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6138653	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs723774	0.90[AMR][1000 genomes]
rs878176	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6138623	PYGB	cis	Whole Blood	GTEx
rs6138623	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138623	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138623	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138623	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	chr20:25605400-25628600	Weak transcription	Left Ventricle	heart
2	chr20:25605400-25630400	Weak transcription	Aorta	Aorta
3	chr20:25605600-25618000	Weak transcription	NH-A	brain
4	chr20:25605600-25619200	Weak transcription	Liver	Liver
5	chr20:25605600-25627000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr20:25605600-25628400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:25605600-25628600	Weak transcription	Colon Smooth Muscle	Colon
8	chr20:25605600-25630200	Weak transcription	Fetal Intestine Large	intestine
9	chr20:25605600-25635000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr20:25606200-25617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:25606200-25626400	Weak transcription	A549	lung
13	chr20:25607800-25623000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25609200-25653400	Weak transcription	Brain Substantia Nigra	brain
15	chr20:25610200-25630400	Weak transcription	Ovary	ovary
16	chr20:25610200-25635600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:25610600-25625000	Weak transcription	HSMMtube	muscle
18	chr20:25610600-25626200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr20:25610600-25630600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr20:25611400-25653200	Weak transcription	Fetal Intestine Small	intestine
21	chr20:25613400-25635000	Weak transcription	Hela-S3	cervix
22	chr20:25613600-25624000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr20:25613600-25635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr20:25613800-25617600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr20:25614200-25626000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr20:25614400-25632400	Weak transcription	Osteobl	bone
27	chr20:25614600-25625800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:25614600-25628400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr20:25614600-25635000	Weak transcription	NHEK	skin
30	chr20:25615000-25617600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:25615000-25617800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:25615000-25618200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:25615000-25619200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr20:25615000-25619600	ZNF genes & repeats	Dnd41	blood
35	chr20:25615200-25618000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr20:25615400-25618000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:25615400-25618400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr20:25615600-25617600	Weak transcription	GM12878-XiMat	blood
39	chr20:25616000-25617800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:25616000-25618800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
41	chr20:25616000-25653600	Weak transcription	Adipose Nuclei	Adipose
42	chr20:25616200-25618200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:25616200-25624400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr20:25616400-25617800	Weak transcription	Stomach Mucosa	stomach
45	chr20:25616400-25618400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:25616600-25617600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25616600-25617600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:25616600-25617800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:25616600-25618200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr20:25616600-25618400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell

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