Variant report

Variant	rs2072964
Chromosome Location	chr20:1099199-1099200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:1099144-1099445	K562	blood:	n/a	n/a
2	CTCF	chr20:1098910-1099293	GM12878	blood:	n/a	n/a
3	MBD4	chr20:1098716-1099581	HepG2	liver:	n/a	n/a
4	TCF12	chr20:1098640-1099725	A549	lung:	n/a	n/a
5	MYC	chr20:1099038-1099260	MCF-7	breast:	n/a	n/a
6	ETS1	chr20:1099000-1099425	K562	blood:	n/a	chr20:1099236-1099246 chr20:1099238-1099247 chr20:1099238-1099247 chr20:1099235-1099251 chr20:1099240-1099249 chr20:1099238-1099247 chr20:1099238-1099247 chr20:1099238-1099247 chr20:1099126-1099135
7	POLR2A	chr20:1098596-1099519	K562	blood:	n/a	n/a
8	SIN3AK20	chr20:1098867-1099621	MCF-7	breast:	n/a	n/a
9	POU2F2	chr20:1098838-1099536	GM12878	blood:	n/a	n/a
10	FOSL2	chr20:1098829-1099719	HepG2	liver:	n/a	n/a
11	PBX3	chr20:1098890-1099456	SK-N-SH	brain:	n/a	n/a
12	YY1	chr20:1098804-1099919	HepG2	liver:	n/a	chr20:1099273-1099285
13	CHD2	chr20:1098858-1099428	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr20:1098812-1099396	Hela-S3	cervix:	n/a	n/a
15	JUND	chr20:1098762-1099593	H1-hESC	embryonic stem cell:	n/a	n/a
16	PAX5	chr20:1099020-1099490	GM12892	blood:	n/a	n/a
17	SRF	chr20:1099009-1099287	GM12878	blood:	n/a	n/a
18	YY1	chr20:1098855-1099596	K562	blood:	n/a	chr20:1099273-1099285
19	TAF1	chr20:1098927-1099407	SK-N-SH	brain:	n/a	n/a
20	SIN3AK20	chr20:1099026-1099413	PANC-1	pancreas:	n/a	n/a
21	RCOR1	chr20:1098885-1099420	GM12878	blood:	n/a	n/a
22	POLR2A	chr20:1098785-1099566	HCT-116	colon:	n/a	n/a
23	ELF1	chr20:1098818-1099445	A549	lung:	n/a	chr20:1099125-1099134 chr20:1099238-1099249 chr20:1099123-1099136 chr20:1099239-1099248
24	RCOR1	chr20:1098654-1099436	K562	blood:	n/a	n/a
25	TEAD4	chr20:1098631-1099285	K562	blood:	n/a	n/a
26	FOXA2	chr20:1098959-1099514	A549	lung:	n/a	n/a
27	POLR2A	chr20:1098649-1099800	PFSK-1	brain:	n/a	n/a
28	USF1	chr20:1098913-1099295	K562	blood:	n/a	n/a
29	TAF1	chr20:1098838-1099535	GM12878	blood:	n/a	n/a
30	ELK1	chr20:1098902-1099381	Hela-S3	cervix:	n/a	chr20:1099238-1099247 chr20:1099238-1099247
31	CTCF	chr20:1099060-1099210	HCPEpiC	choroid plexus:	n/a	n/a
32	MAX	chr20:1098865-1099663	K562	blood:	n/a	n/a
33	RUNX3	chr20:1098873-1099784	GM12878	blood:	n/a	n/a
34	MXI1	chr20:1098570-1100368	IMR90	lung:	n/a	n/a
35	SP1	chr20:1098653-1099600	A549	lung:	n/a	chr20:1098999-1099013 chr20:1099566-1099580 chr20:1099142-1099152
36	TEAD4	chr20:1098855-1099337	H1-hESC	embryonic stem cell:	n/a	n/a
37	JUN	chr20:1098617-1099722	K562	blood:	n/a	n/a
38	POLR2A	chr20:1098865-1099587	A549	lung:	n/a	n/a
39	IRF1	chr20:1098734-1099989	K562	blood:	n/a	chr20:1099139-1099153
40	POLR2A	chr20:1098611-1099978	GM12878	blood:	n/a	n/a
41	GTF2B	chr20:1098976-1099244	K562	blood:	n/a	n/a
42	POLR2A	chr20:1098833-1099724	GM15510	blood:	n/a	n/a
43	EP300	chr20:1098812-1099557	A549	lung:	n/a	chr20:1099239-1099246 chr20:1099153-1099166
44	POLR2A	chr20:1098837-1099527	K562	blood:	n/a	n/a
45	YY1	chr20:1098842-1099633	SK-N-SH_RA	brain:	n/a	chr20:1099273-1099285
46	FOXA1	chr20:1098858-1099550	HepG2	liver:	n/a	n/a
47	FOXM1	chr20:1098845-1099291	GM12878	blood:	n/a	n/a
48	ELF1	chr20:1098700-1099571	HepG2	liver:	n/a	chr20:1099125-1099134 chr20:1099238-1099249 chr20:1099123-1099136 chr20:1099239-1099248
49	POLR2A	chr20:1098476-1101083	HepG2	liver:	n/a	n/a
50	CCNT2	chr20:1098998-1099631	K562	blood:	n/a	n/a

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	chr11:62609153..62610033-chr20:1099017..1099920,2	Hela-S3	cervix:

Variant related genes	Relation type
PSMF1	TF binding region
ENSG00000261971	Chromatin interaction
ENSG00000125818	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11908561	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1803415	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883522	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2072961	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072962	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072963	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	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179450	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2235587	0.84[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2268065	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284371	0.86[JPT][hapmap]
rs2284372	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284375	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3787572	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4142353	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4289256	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040009	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6040024	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6040066	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040108	0.84[ASN][1000 genomes]
rs6040155	0.84[JPT][hapmap]
rs6074148	0.95[JPT][hapmap]
rs6077826	0.86[JPT][hapmap]
rs6077915	0.80[JPT][hapmap]
rs6133957	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6133961	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6133989	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[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

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	chr20:1098600-1099200	Flanking Active TSS	Liver	Liver
15	chr20:1098600-1099600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:1098600-1099800	Active TSS	Esophagus	oesophagus
17	chr20:1098600-1099800	Active TSS	Fetal Lung	lung
18	chr20:1098600-1099800	Active TSS	Fetal Muscle Trunk	muscle
19	chr20:1098600-1100000	Active TSS	Left Ventricle	heart
20	chr20:1098600-1100000	Active TSS	Ovary	ovary
21	chr20:1098600-1100000	Active TSS	Pancreas	Pancrea
22	chr20:1098600-1100000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr20:1098600-1100000	Active TSS	Psoas Muscle	Psoas
24	chr20:1098600-1100200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr20:1098600-1100200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr20:1098600-1100200	Active TSS	Right Atrium	heart
27	chr20:1098600-1100400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr20:1098600-1100400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:1098600-1100600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:1098800-1099400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr20:1098800-1099600	Active TSS	Stomach Smooth Muscle	stomach
32	chr20:1098800-1099800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr20:1098800-1099800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr20:1098800-1099800	Active TSS	Brain Angular Gyrus	brain
35	chr20:1098800-1099800	Active TSS	Brain Anterior Caudate	brain
36	chr20:1098800-1099800	Active TSS	Brain Cingulate Gyrus	brain
37	chr20:1098800-1099800	Active TSS	Brain Hippocampus Middle	brain
38	chr20:1098800-1099800	Active TSS	Fetal Heart	heart
39	chr20:1098800-1099800	Active TSS	Fetal Stomach	stomach
40	chr20:1098800-1099800	Active TSS	Right Ventricle	heart
41	chr20:1098800-1099800	Active TSS	K562	blood
42	chr20:1098800-1100000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr20:1098800-1100000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr20:1098800-1100000	Active TSS	Colon Smooth Muscle	Colon
45	chr20:1098800-1100000	Active TSS	Fetal Intestine Large	intestine
46	chr20:1098800-1100000	Active TSS	Gastric	stomach
47	chr20:1098800-1100000	Active TSS	Lung	lung
48	chr20:1098800-1100000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr20:1098800-1100000	Active TSS	NHLF	lung
50	chr20:1098800-1100200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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