Variant report

Variant	rs62241279
Chromosome Location	chr3:19988567-19988568
allele	A/G
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	POLR2A	chr3:19987362-19989595	K562	blood:	n/a	n/a
2	PAX5	chr3:19988354-19988680	GM12878	blood:	n/a	chr3:19988633-19988642
3	GABPA	chr3:19988184-19989088	SK-N-SH	brain:	n/a	chr3:19988538-19988545
4	HCFC1	chr3:19987605-19989689	K562	blood:	n/a	n/a
5	GABPA	chr3:19988362-19988740	H1-hESC	embryonic stem cell:	n/a	chr3:19988538-19988545
6	RUNX3	chr3:19987795-19989519	GM12878	blood:	n/a	n/a
7	USF2	chr3:19988281-19988662	HepG2	liver:	n/a	chr3:19988614-19988630 chr3:19988464-19988475
8	REST	chr3:19988547-19988786	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr3:19987558-19989602	GM18951	blood:	n/a	n/a
10	POLR2A	chr3:19986887-19989909	GM12891	blood:	n/a	n/a
11	STAT1	chr3:19987955-19989668	GM12878	blood:	n/a	chr3:19988530-19988542 chr3:19989252-19989264 chr3:19989188-19989197 chr3:19988321-19988329 chr3:19989110-19989122
12	TCF12	chr3:19988391-19988815	GM12878	blood:	n/a	n/a
13	FOS	chr3:19988327-19988670	MCF10A-Er-Src	breast:	n/a	n/a
14	FOSL2	chr3:19988232-19988732	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr3:19987338-19989938	MCF-7	breast:	n/a	n/a
16	POU2F2	chr3:19988429-19988757	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:19988297-19989442	ECC-1	luminal epithelium:	n/a	n/a
18	YY1	chr3:19987952-19988608	K562	blood:	n/a	chr3:19987999-19988008 chr3:19988151-19988159
19	ZBTB33	chr3:19988244-19988771	A549	lung:	n/a	n/a
20	EGR1	chr3:19988040-19988966	K562	blood:	n/a	chr3:19988337-19988347 chr3:19988633-19988642 chr3:19988244-19988254 chr3:19988611-19988621
21	EP300	chr3:19988051-19989533	GM12878	blood:	n/a	chr3:19989189-19989198 chr3:19988330-19988346 chr3:19988621-19988637
22	EGR1	chr3:19988264-19988740	H1-hESC	embryonic stem cell:	n/a	chr3:19988337-19988347 chr3:19988633-19988642 chr3:19988611-19988621
23	HEY1	chr3:19987858-19989594	K562	blood:	n/a	n/a
24	GABPA	chr3:19988286-19988975	A549	lung:	n/a	chr3:19988538-19988545
25	ETS1	chr3:19988272-19988954	K562	blood:	n/a	chr3:19988633-19988650 chr3:19988634-19988644 chr3:19988633-19988642 chr3:19988633-19988650 chr3:19988609-19988620
26	CREB1	chr3:19988089-19989745	HepG2	liver:	n/a	n/a
27	BCL3	chr3:19987604-19988689	A549	lung:	n/a	chr3:19988323-19988332 chr3:19988611-19988624 chr3:19988633-19988642
28	SIX5	chr3:19988448-19988745	A549	lung:	n/a	n/a
29	CEBPD	chr3:19988180-19988727	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:19988117-19989553	MCF-7	breast:	n/a	n/a
31	ZEB1	chr3:19988258-19988727	GM12878	blood:	n/a	n/a
32	NFIC	chr3:19988190-19988781	GM12878	blood:	n/a	n/a
33	MAX	chr3:19987921-19989653	HepG2	liver:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
34	GABPA	chr3:19988373-19988781	H1-hESC	embryonic stem cell:	n/a	chr3:19988538-19988545
35	JUN	chr3:19987484-19988866	K562	blood:	n/a	n/a
36	MYC	chr3:19988297-19988639	K562	blood:	n/a	chr3:19988609-19988619
37	SMARCC1	chr3:19986964-19989766	Hela-S3	cervix:	n/a	chr3:19989188-19989197 chr3:19989189-19989198
38	NFIC	chr3:19988124-19988671	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr3:19988033-19989755	K562	blood:	n/a	n/a
40	POLR2A	chr3:19987474-19989718	GM12878	blood:	n/a	n/a
41	USF2	chr3:19988148-19989015	H1-hESC	embryonic stem cell:	n/a	chr3:19988614-19988630 chr3:19988464-19988475
42	MAX	chr3:19988142-19989678	MCF-7	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
43	RAD21	chr3:19988299-19988736	K562	blood:	n/a	chr3:19988622-19988635
44	MYC	chr3:19988199-19989610	MCF10A-Er-Src	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
45	ATF3	chr3:19988313-19988710	K562	blood:	n/a	n/a
46	FOXM1	chr3:19987637-19989053	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:19987476-19989652	U87	brain:	n/a	n/a
48	POLR2A	chr3:19987594-19989784	GM18505	blood:	n/a	n/a
49	HMGN3	chr3:19987829-19989561	K562	blood:	n/a	chr3:19989190-19989199
50	YY1	chr3:19988002-19989624	NT2-D1	testis:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19988151-19988159 chr3:19989258-19989280

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
4	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
5	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
6	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
7	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
8	chr1:155107729..155108614-chr3:19988180..19988972,2	Hela-S3	cervix:
9	chr3:19188168..19190474-chr3:19988134..19989911,2	MCF-7	breast:
10	chr14:24899081..24899637-chr3:19988552..19989514,2	Hela-S3	cervix:
11	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
EFHB	TF binding region
RAB5A	TF binding region
HSPA8P18	TF binding region
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000163576	Chromatin interaction
ENSG00000183960	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000100441	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510497	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[ASN][1000 genomes]
rs12490848	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497549	1.00[ASN][1000 genomes]
rs17181337	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796230	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365374	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597881	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241539	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398451	1.00[ASN][1000 genomes]
rs45542931	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858662	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858664	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241295	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243065	1.00[ASN][1000 genomes]
rs62243074	1.00[ASN][1000 genomes]
rs62243075	1.00[ASN][1000 genomes]
rs62243076	1.00[ASN][1000 genomes]
rs73032477	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034166	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 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	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
2	chr3:19987000-19989600	Active TSS	Liver	Liver
3	chr3:19987200-19989000	Active TSS	HepG2	liver
4	chr3:19987200-19989800	Active TSS	Pancreas	Pancrea
5	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:19987200-19990400	Active TSS	Placenta	Placenta
7	chr3:19987200-19990600	Active TSS	K562	blood
8	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:19987400-19988800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:19987400-19989000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:19987400-19989200	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr3:19987400-19989400	Active TSS	Brain Anterior Caudate	brain
13	chr3:19987400-19989400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:19987400-19989400	Active TSS	Rectal Smooth Muscle	rectum
15	chr3:19987400-19989800	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr3:19987400-19990000	Active TSS	Brain Germinal Matrix	brain
17	chr3:19987400-19990000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:19987400-19990000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:19987400-19990000	Active TSS	A549	lung
20	chr3:19987400-19990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:19987400-19990200	Active TSS	HSMM	muscle
22	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
23	chr3:19987400-19990800	Active TSS	Right Atrium	heart
24	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
25	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:19987600-19988800	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr3:19987600-19989000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:19987600-19989000	Active TSS	Fetal Brain Male	brain
29	chr3:19987600-19989400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:19987600-19989400	Active TSS	Fetal Brain Female	brain
31	chr3:19987600-19989600	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:19987600-19989800	Active TSS	Brain Hippocampus Middle	brain
33	chr3:19987600-19989800	Active TSS	Left Ventricle	heart
34	chr3:19987600-19989800	Active TSS	Lung	lung
35	chr3:19987600-19990000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:19987600-19990000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:19987600-19990000	Active TSS	Ovary	ovary
38	chr3:19987600-19990000	Active TSS	Thymus	Thymus
39	chr3:19987600-19990200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:19987600-19990200	Active TSS	Colon Smooth Muscle	Colon
41	chr3:19987600-19990400	Active TSS	Colonic Mucosa	Colon
42	chr3:19987600-19990400	Active TSS	Fetal Kidney	kidney
43	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr3:19987600-19991000	Active TSS	NHLF	lung
45	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:19987800-19989200	Active TSS	Primary T cells from cord blood	blood
47	chr3:19987800-19989800	Active TSS	Esophagus	oesophagus
48	chr3:19987800-19989800	Active TSS	Fetal Heart	heart
49	chr3:19987800-19989800	Active TSS	Small Intestine	intestine
50	chr3:19987800-19990000	Active TSS	Aorta	Aorta

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