Variant report

Variant	rs6138578
Chromosome Location	chr20:25452640-25452641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11697535	0.89[EUR][1000 genomes]
rs11697736	0.89[EUR][1000 genomes]
rs13045549	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34005053	0.89[EUR][1000 genomes]
rs34056528	1.00[EUR][1000 genomes]
rs35000100	1.00[AFR][1000 genomes]
rs35464704	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35705198	1.00[EUR][1000 genomes]
rs6132841	0.84[ASN][1000 genomes]
rs6132843	0.83[ASN][1000 genomes]
rs6138567	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138585	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25425600-25453200	Weak transcription	Small Intestine	intestine
2	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
3	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:25429800-25458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
6	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
8	chr20:25435600-25459000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr20:25435800-25465600	Weak transcription	NH-A	brain
10	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr20:25437800-25454600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr20:25438000-25456400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr20:25438400-25455400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:25438600-25453200	Strong transcription	Fetal Intestine Small	intestine
15	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:25438800-25455000	Strong transcription	Fetal Intestine Large	intestine
17	chr20:25438800-25472600	Strong transcription	HepG2	liver
18	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
19	chr20:25441800-25455000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr20:25442200-25460000	Weak transcription	Brain Angular Gyrus	brain
21	chr20:25443200-25459000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:25443800-25457400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr20:25446000-25459600	Weak transcription	Fetal Brain Male	brain
24	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
25	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr20:25446400-25455200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
28	chr20:25446600-25457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
30	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr20:25448400-25456600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr20:25448400-25458800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:25448400-25459000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:25448800-25453600	Weak transcription	Brain Substantia Nigra	brain
36	chr20:25448800-25464600	Weak transcription	HUVEC	blood vessel
37	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:25449000-25459000	Weak transcription	Adipose Nuclei	Adipose
39	chr20:25449000-25459400	Weak transcription	Right Ventricle	heart
40	chr20:25449400-25459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr20:25449800-25456800	Weak transcription	Lung	lung
42	chr20:25450000-25463000	Strong transcription	Liver	Liver
43	chr20:25450200-25455400	Strong transcription	Fetal Lung	lung
44	chr20:25450600-25456600	Weak transcription	Esophagus	oesophagus
45	chr20:25450600-25456800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr20:25450600-25456800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr20:25450800-25454600	Weak transcription	Brain Hippocampus Middle	brain
48	chr20:25450800-25456800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:25450800-25456800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr20:25450800-25457200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links