Variant report

Variant	rs1989400
Chromosome Location	chr20:1124560-1124561
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	chr20:1120810..1122825-chr20:1122949..1124909,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1883522	0.93[ASN][1000 genomes]
rs2179449	0.87[ASN][1000 genomes]
rs2179450	0.93[ASN][1000 genomes]
rs4142353	0.85[ASN][1000 genomes]
rs4289256	0.85[ASN][1000 genomes]
rs6040066	0.85[ASN][1000 genomes]
rs6040108	0.93[ASN][1000 genomes]
rs6133989	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1989400	PSMF1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100400-1132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr20:1102200-1128600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr20:1103600-1127800	Weak transcription	Fetal Heart	heart
5	chr20:1103600-1130800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:1103600-1130800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:1104600-1125600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:1104600-1128600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr20:1104600-1135800	Strong transcription	Dnd41	blood
10	chr20:1112200-1137400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr20:1113800-1130200	Strong transcription	HepG2	liver
13	chr20:1113800-1135200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:1114000-1138000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:1115000-1128800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:1115200-1128800	Strong transcription	A549	lung
18	chr20:1115200-1129000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:1115200-1129000	Strong transcription	Adipose Nuclei	Adipose
20	chr20:1115200-1153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:1115800-1137800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr20:1116000-1141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:1116600-1124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr20:1116600-1126800	Weak transcription	Small Intestine	intestine
25	chr20:1116600-1127200	Weak transcription	Right Ventricle	heart
26	chr20:1116600-1144600	Weak transcription	Stomach Mucosa	stomach
27	chr20:1116800-1141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr20:1117000-1126000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr20:1117000-1130200	Weak transcription	Psoas Muscle	Psoas
30	chr20:1117000-1141200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr20:1117000-1141600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:1117200-1125600	Weak transcription	Esophagus	oesophagus
33	chr20:1117200-1125800	Weak transcription	Colonic Mucosa	Colon
34	chr20:1117200-1125800	Weak transcription	Gastric	stomach
35	chr20:1117200-1127200	Weak transcription	Aorta	Aorta
36	chr20:1117200-1144600	Weak transcription	Hela-S3	cervix
37	chr20:1117400-1125400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:1117400-1127000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr20:1117800-1124600	Weak transcription	Thymus	Thymus
40	chr20:1117800-1125600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr20:1118000-1125800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr20:1118000-1126600	Weak transcription	Brain Substantia Nigra	brain
43	chr20:1118000-1127000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr20:1118000-1127200	Weak transcription	Pancreas	Pancrea
45	chr20:1118000-1128400	Strong transcription	Liver	Liver
46	chr20:1118000-1134000	Weak transcription	HSMMtube	muscle
47	chr20:1118000-1135400	Weak transcription	Fetal Brain Male	brain
48	chr20:1118000-1135600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr20:1118200-1126000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr20:1118200-1126200	Weak transcription	Osteobl	bone

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