Variant report

Variant	rs2072963
Chromosome Location	chr20:1099294-1099295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:3109089..3109876-chr20:1098820..1099738,2	HCT-116	colon:
2	chr15:65596673..65597233-chr20:1098833..1099436,3	NB4	blood:
3	chr20:1093479..1095284-chr20:1095646..1099615,3	K562	blood:
4	chr20:1099167..1103189-chr20:1144544..1147545,4	K562	blood:
5	chr19:10676245..10676821-chr20:1099243..1099823,2	NB4	blood:
6	chr11:62609153..62610033-chr20:1099017..1099920,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000125818	Chromatin interaction
ENSG00000129347	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000261971	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11908561	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16991645	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1803415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883522	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2072961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072964	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179450	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2235587	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]
rs2268065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284371	0.91[JPT][hapmap]
rs2284372	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284375	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3787572	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142353	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4289256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4813923	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6040009	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6040024	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6040066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040108	0.85[ASN][1000 genomes]
rs6040155	0.80[JPT][hapmap]
rs6074148	0.90[JPT][hapmap]
rs6077826	0.90[JPT][hapmap]
rs6077915	0.81[JPT][hapmap]
rs6133957	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6133961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6133989	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8118249	0.80[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1098200-1100000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr20:1098400-1099600	Active TSS	Colonic Mucosa	Colon
3	chr20:1098400-1099800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:1098400-1099800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr20:1098400-1099800	Active TSS	Rectal Smooth Muscle	rectum
6	chr20:1098400-1100000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:1098400-1100000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:1098400-1100000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:1098400-1100000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr20:1098400-1100000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:1098400-1100200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr20:1098400-1100400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:1098400-1101000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr20:1098600-1099600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:1098600-1099800	Active TSS	Esophagus	oesophagus
16	chr20:1098600-1099800	Active TSS	Fetal Lung	lung
17	chr20:1098600-1099800	Active TSS	Fetal Muscle Trunk	muscle
18	chr20:1098600-1100000	Active TSS	Left Ventricle	heart
19	chr20:1098600-1100000	Active TSS	Ovary	ovary
20	chr20:1098600-1100000	Active TSS	Pancreas	Pancrea
21	chr20:1098600-1100000	Active TSS	Placenta Amnion	Placenta Amnion
22	chr20:1098600-1100000	Active TSS	Psoas Muscle	Psoas
23	chr20:1098600-1100200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr20:1098600-1100200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr20:1098600-1100200	Active TSS	Right Atrium	heart
26	chr20:1098600-1100400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr20:1098600-1100400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr20:1098600-1100600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:1098800-1099400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:1098800-1099600	Active TSS	Stomach Smooth Muscle	stomach
31	chr20:1098800-1099800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr20:1098800-1099800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr20:1098800-1099800	Active TSS	Brain Angular Gyrus	brain
34	chr20:1098800-1099800	Active TSS	Brain Anterior Caudate	brain
35	chr20:1098800-1099800	Active TSS	Brain Cingulate Gyrus	brain
36	chr20:1098800-1099800	Active TSS	Brain Hippocampus Middle	brain
37	chr20:1098800-1099800	Active TSS	Fetal Heart	heart
38	chr20:1098800-1099800	Active TSS	Fetal Stomach	stomach
39	chr20:1098800-1099800	Active TSS	Right Ventricle	heart
40	chr20:1098800-1099800	Active TSS	K562	blood
41	chr20:1098800-1100000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr20:1098800-1100000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr20:1098800-1100000	Active TSS	Colon Smooth Muscle	Colon
44	chr20:1098800-1100000	Active TSS	Fetal Intestine Large	intestine
45	chr20:1098800-1100000	Active TSS	Gastric	stomach
46	chr20:1098800-1100000	Active TSS	Lung	lung
47	chr20:1098800-1100000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr20:1098800-1100000	Active TSS	NHLF	lung
49	chr20:1098800-1100200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr20:1098800-1100200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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