Variant report

Variant	rs6078413
Chromosome Location	chr20:1249345-1249346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1204614..1208313-chr20:1245857..1250887,4	K562	blood:
2	chr20:1249007..1250962-chr20:1262132..1264748,2	K562	blood:
3	chr20:1249007..1251870-chr20:1263248..1267387,3	K562	blood:

Variant related genes	Relation type
ENSG00000244588	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12480861	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16992733	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16992790	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923876	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6040904	0.86[ASN][1000 genomes]
rs6074333	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078248	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6078274	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6078316	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073641	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs753949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653633	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv518957	chr20:1195784-1250463	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1067360	chr20:1245753-1283508	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1246400-1249600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr20:1247600-1249400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:1247600-1253200	Weak transcription	Aorta	Aorta
4	chr20:1247800-1261000	Weak transcription	Right Ventricle	heart
5	chr20:1247800-1262000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:1248000-1249600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr20:1248000-1251400	Enhancers	K562	blood
8	chr20:1248000-1252200	Weak transcription	Ovary	ovary
9	chr20:1248000-1252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr20:1248000-1253200	Weak transcription	Lung	lung
11	chr20:1248000-1253200	Weak transcription	HSMM	muscle
12	chr20:1248000-1253400	Weak transcription	Brain Germinal Matrix	brain
13	chr20:1248000-1253600	Weak transcription	NHDF-Ad	bronchial
14	chr20:1248000-1255800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:1248000-1260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:1248000-1260800	Weak transcription	Osteobl	bone
17	chr20:1248000-1266800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr20:1248000-1271800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
20	chr20:1248200-1249400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:1248200-1249400	Enhancers	Stomach Smooth Muscle	stomach
22	chr20:1248200-1250200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr20:1248200-1251600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:1248200-1252600	Weak transcription	HSMMtube	muscle
25	chr20:1248200-1252800	Weak transcription	Fetal Muscle Leg	muscle
26	chr20:1248200-1253400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr20:1248200-1253400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:1248200-1253400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr20:1248200-1255200	Weak transcription	Fetal Brain Female	brain
30	chr20:1248200-1255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:1248200-1260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr20:1248200-1260600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr20:1248200-1265000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr20:1248200-1277400	Weak transcription	Fetal Stomach	stomach
35	chr20:1248200-1281200	Weak transcription	NHEK	skin
36	chr20:1248400-1249400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr20:1248400-1249800	Enhancers	Placenta	Placenta
38	chr20:1248400-1253000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:1248400-1253400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr20:1248400-1255600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr20:1248400-1261400	Weak transcription	Colon Smooth Muscle	Colon
42	chr20:1248600-1250200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr20:1248600-1253600	Weak transcription	Brain Hippocampus Middle	brain
44	chr20:1248600-1266800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr20:1248800-1250000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr20:1248800-1251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr20:1248800-1253200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr20:1248800-1253400	Weak transcription	Gastric	stomach
49	chr20:1248800-1258000	Weak transcription	NHLF	lung
50	chr20:1248800-1263600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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