Variant report

Variant	rs6083820
Chromosome Location	chr20:25354178-25354179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13040130	0.81[AMR][1000 genomes]
rs2260197	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs404148	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs449801	0.84[EUR][1000 genomes]
rs6076347	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083810	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083841	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62213729	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic 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	16 gene(s)	inside rSNPs	diseases
17	nsv964440	chr20:25351740-25387631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6083820	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6083820	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6083820	ABHD12	cis	multi-tissue	Pritchard
rs6083820	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
2	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
3	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr20:25337000-25370000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:25337400-25355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25337600-25354200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:25337600-25362800	Weak transcription	Spleen	Spleen
8	chr20:25338000-25369400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:25338200-25359000	Weak transcription	Fetal Intestine Large	intestine
10	chr20:25339400-25359600	Weak transcription	Lung	lung
11	chr20:25341800-25357600	Weak transcription	Ovary	ovary
12	chr20:25342200-25354600	Weak transcription	Dnd41	blood
13	chr20:25342200-25361800	Weak transcription	Primary B cells from cord blood	blood
14	chr20:25342200-25362600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr20:25342200-25370000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr20:25342400-25355600	Weak transcription	A549	lung
17	chr20:25342400-25357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:25343800-25370000	Weak transcription	Small Intestine	intestine
19	chr20:25345200-25369800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr20:25345800-25354200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr20:25345800-25357600	Weak transcription	Right Atrium	heart
22	chr20:25345800-25359400	Weak transcription	Left Ventricle	heart
23	chr20:25345800-25359600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr20:25345800-25361600	Weak transcription	K562	blood
25	chr20:25345800-25363200	Weak transcription	Esophagus	oesophagus
26	chr20:25345800-25369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr20:25345800-25370000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr20:25345800-25370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:25346200-25357600	Weak transcription	HepG2	liver
30	chr20:25346200-25362800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr20:25346600-25355200	Weak transcription	Gastric	stomach
32	chr20:25347600-25357600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr20:25350600-25357000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr20:25351400-25357000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr20:25351400-25359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:25351400-25369600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr20:25351800-25370000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:25352000-25356000	Weak transcription	Pancreas	Pancrea
39	chr20:25352000-25356800	Weak transcription	Brain Angular Gyrus	brain
40	chr20:25352000-25357200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr20:25352000-25359600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr20:25352000-25359600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr20:25352000-25362600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr20:25352400-25355600	Weak transcription	Brain Substantia Nigra	brain
45	chr20:25352400-25357000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr20:25352600-25356000	Weak transcription	Brain Hippocampus Middle	brain
47	chr20:25352600-25356200	Weak transcription	Brain Anterior Caudate	brain
48	chr20:25353000-25370000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr20:25353600-25354200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr20:25353600-25354200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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