Variant report

Variant	rs12481409
Chromosome Location	chr20:25436466-25436467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11696666	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11699872	0.84[EUR][1000 genomes]
rs11700213	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12625748	0.86[EUR][1000 genomes]
rs2050097	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072976	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281212	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35084391	0.86[EUR][1000 genomes]
rs3736720	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764694	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6107050	0.83[ASN][1000 genomes]
rs6115202	0.89[ASN][1000 genomes]
rs66807280	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68053392	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73109499	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73597807	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9305141	0.86[ASN][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	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	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
14	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
15	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
16	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25402800-25445200	Weak transcription	NHDF-Ad	bronchial
2	chr20:25412600-25440200	Weak transcription	Placenta	Placenta
3	chr20:25418200-25436600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr20:25418200-25445200	Weak transcription	HSMM	muscle
5	chr20:25418800-25439400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:25425600-25453200	Weak transcription	Small Intestine	intestine
7	chr20:25426400-25450200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
9	chr20:25427400-25442400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr20:25427600-25442200	Weak transcription	GM12878-XiMat	blood
11	chr20:25427600-25446200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr20:25428600-25438600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:25429600-25441000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr20:25429800-25458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
17	chr20:25430400-25442000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr20:25431200-25447400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:25431600-25436600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr20:25431800-25442000	Weak transcription	Brain Angular Gyrus	brain
21	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr20:25432200-25436600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr20:25432200-25436600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr20:25432200-25437000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr20:25432400-25436600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr20:25432400-25436600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:25432400-25440600	Weak transcription	Colonic Mucosa	Colon
28	chr20:25432400-25450400	Strong transcription	Thymus	Thymus
29	chr20:25432600-25436600	Strong transcription	Liver	Liver
30	chr20:25432600-25436600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr20:25432600-25436600	Strong transcription	HepG2	liver
32	chr20:25432600-25436800	Strong transcription	Fetal Muscle Leg	muscle
33	chr20:25432600-25452400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr20:25433000-25436600	Strong transcription	Fetal Intestine Small	intestine
35	chr20:25433000-25436800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr20:25433200-25444200	Weak transcription	Fetal Brain Male	brain
37	chr20:25433200-25445200	Weak transcription	Right Atrium	heart
38	chr20:25433600-25436600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr20:25434000-25447800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr20:25434200-25447400	Weak transcription	HUVEC	blood vessel
41	chr20:25434400-25439000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
43	chr20:25435400-25438600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:25435600-25438400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr20:25435600-25459000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr20:25435800-25450200	Weak transcription	Fetal Kidney	kidney
47	chr20:25435800-25465600	Weak transcription	NH-A	brain
48	chr20:25436000-25438600	Weak transcription	Pancreas	Pancrea
49	chr20:25436000-25439600	Weak transcription	Right Ventricle	heart
50	chr20:25436000-25445200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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