Variant report

Variant	rs6040293
Chromosome Location	chr20:1153225-1153226
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	chr20:1149468..1153458-chr20:1155297..1158129,3	K562	blood:
2	chr20:1151539..1154295-chr20:1159812..1162890,3	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2072965	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2300185	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2300186	0.92[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3087751	0.86[YRI][hapmap]
rs3746814	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813044	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813945	0.96[CEU][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6040199	0.86[YRI][hapmap]
rs6040222	0.90[JPT][hapmap]
rs6074191	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6077930	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6134051	0.95[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs742429	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:1115200-1153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:1130000-1157800	Strong transcription	Duodenum Mucosa	Duodenum
5	chr20:1133800-1153800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:1135600-1159800	Weak transcription	Fetal Heart	heart
7	chr20:1137200-1154400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr20:1137400-1157800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr20:1137400-1157800	Strong transcription	Thymus	Thymus
10	chr20:1137400-1159200	Strong transcription	Primary T cells from cord blood	blood
11	chr20:1138800-1154600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr20:1138800-1156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr20:1138800-1158800	Strong transcription	Fetal Stomach	stomach
14	chr20:1139000-1157800	Strong transcription	Liver	Liver
15	chr20:1139000-1157800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr20:1139000-1157800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr20:1139000-1158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:1139200-1155200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:1139600-1157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr20:1139800-1153800	Strong transcription	A549	lung
21	chr20:1139800-1158200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr20:1140000-1157800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr20:1140200-1153800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr20:1140200-1154000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:1140200-1154800	Strong transcription	Fetal Intestine Large	intestine
26	chr20:1140200-1156400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr20:1140200-1156800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr20:1140200-1156800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:1140200-1157600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr20:1140200-1157800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr20:1140200-1157800	Strong transcription	Fetal Muscle Leg	muscle
32	chr20:1140200-1158400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:1140200-1159000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr20:1140400-1156800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr20:1140400-1157200	Strong transcription	Placenta	Placenta
36	chr20:1140400-1158600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr20:1140400-1159200	Strong transcription	Adipose Nuclei	Adipose
38	chr20:1140600-1156400	Strong transcription	Brain Angular Gyrus	brain
39	chr20:1140600-1157000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr20:1140600-1157800	Strong transcription	Brain Anterior Caudate	brain
41	chr20:1140800-1159000	Strong transcription	Fetal Brain Female	brain
42	chr20:1141200-1157200	Strong transcription	Primary B cells from cord blood	blood
43	chr20:1143000-1161600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr20:1143400-1154400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:1143400-1156600	Strong transcription	Aorta	Aorta
46	chr20:1143400-1157200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr20:1143600-1154000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr20:1143600-1154400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:1143600-1157800	Strong transcription	Brain Hippocampus Middle	brain
50	chr20:1143800-1159200	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links