Variant report

Variant	rs2235587
Chromosome Location	chr20:1115919-1115920
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:25)

rs_ID	r²[population]
rs11908561	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1803415	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1883522	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs2072961	1.00[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2072962	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2072963	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2072964	0.84[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2179449	1.00[CEU][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179450	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs2268065	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2284371	0.82[JPT][hapmap]
rs2284372	0.84[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2284375	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3787572	1.00[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4142353	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4289256	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4813923	0.81[EUR][1000 genomes]
rs6040009	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6040024	0.84[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6040066	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6074148	0.81[JPT][hapmap]
rs6077826	0.81[JPT][hapmap]
rs6133957	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6133961	1.00[CEU][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6133989	0.98[AMR][1000 genomes];0.99[EUR][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

No data

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	chr20:1100800-1122200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:1102200-1128600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:1103600-1127800	Weak transcription	Fetal Heart	heart
6	chr20:1103600-1130800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr20:1103600-1130800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:1104200-1122400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr20:1104200-1122600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:1104600-1125600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr20:1104600-1128600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr20:1104600-1135800	Strong transcription	Dnd41	blood
13	chr20:1105200-1121600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:1105400-1122800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr20:1105600-1122800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:1105800-1122400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr20:1105800-1122600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:1110800-1116600	Weak transcription	Fetal Brain Male	brain
19	chr20:1112000-1116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr20:1112200-1137400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr20:1112400-1122400	Strong transcription	Primary B cells from cord blood	blood
22	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr20:1112800-1123000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr20:1113600-1122000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr20:1113800-1130200	Strong transcription	HepG2	liver
26	chr20:1113800-1135200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr20:1114000-1116200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:1114000-1138000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:1114600-1116600	Strong transcription	Stomach Mucosa	stomach
31	chr20:1114600-1117800	Strong transcription	NHEK	skin
32	chr20:1114600-1117800	Strong transcription	NHLF	lung
33	chr20:1114600-1121800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr20:1114800-1118400	Strong transcription	GM12878-XiMat	blood
35	chr20:1114800-1120800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr20:1114800-1122600	Strong transcription	Fetal Thymus	thymus
37	chr20:1114800-1122800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr20:1114800-1122800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr20:1115000-1116800	Strong transcription	Liver	Liver
40	chr20:1115000-1117200	Strong transcription	Esophagus	oesophagus
41	chr20:1115000-1117200	Strong transcription	Fetal Intestine Small	intestine
42	chr20:1115000-1117800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr20:1115000-1117800	Strong transcription	Brain Angular Gyrus	brain
44	chr20:1115000-1117800	Strong transcription	Thymus	Thymus
45	chr20:1115000-1118000	Strong transcription	Brain Cingulate Gyrus	brain
46	chr20:1115000-1118000	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr20:1115000-1118000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr20:1115000-1118200	Strong transcription	Osteobl	bone
49	chr20:1115000-1119000	Strong transcription	Colon Smooth Muscle	Colon
50	chr20:1115000-1119600	Strong transcription	H1 Cell Line	embryonic stem cell

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