Variant report

Variant	rs59262883
Chromosome Location	chr19:55850763-55850764
allele	G/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	RELA	chr19:55850103-55851253	GM18951	blood:	n/a	n/a
2	NRF1	chr19:55850498-55850968	K562	blood:	n/a	n/a
3	MAX	chr19:55849978-55851223	H1-hESC	embryonic stem cell:	n/a	chr19:55850989-55850998
4	PBX3	chr19:55850439-55851358	GM12878	blood:	n/a	chr19:55851125-55851134 chr19:55851163-55851183 chr19:55850787-55850807 chr19:55850938-55850947 chr19:55850923-55850943
5	CTCF	chr19:55850700-55850850	HRE	kidney:	n/a	n/a
6	CCNT2	chr19:55850049-55851428	K562	blood:	n/a	n/a
7	EP300	chr19:55850041-55851033	Hela-S3	cervix:	n/a	n/a
8	BRCA1	chr19:55850253-55851230	HepG2	liver:	n/a	chr19:55850508-55850517
9	RAD21	chr19:55850280-55850929	IMR90	lung:	n/a	n/a
10	POLR2A	chr19:55850320-55853763	K562	blood:	n/a	n/a
11	CTCF	chr19:55850700-55850850	GM12873	blood:	n/a	n/a
12	CTCF	chr19:55850613-55850879	Pancreas_OC	pancreas:	n/a	n/a
13	SP2	chr19:55850612-55851353	K562	blood:	n/a	chr19:55850971-55850986 chr19:55851125-55851135 chr19:55851006-55851029 chr19:55850921-55850944 chr19:55850785-55850808 chr19:55851178-55851188 chr19:55851161-55851184
14	CTCF	chr19:55850660-55850810	GM12867	blood:	n/a	n/a
15	POLR2A	chr19:55849719-55851490	H1-hESC	embryonic stem cell:	n/a	n/a
16	HA-E2F1	chr19:55849937-55851373	MCF-7	breast:	n/a	chr19:55851332-55851341 chr19:55850655-55850667 chr19:55851053-55851062
17	JUN	chr19:55849822-55852421	K562	blood:	n/a	chr19:55850212-55850225 chr19:55850654-55850663 chr19:55851126-55851135
18	FOXP2	chr19:55850070-55851206	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr19:55850417-55850796	GM12878	blood:	n/a	n/a
20	CHD1	chr19:55850411-55851329	GM12878	blood:	n/a	n/a
21	MAX	chr19:55849880-55851712	ECC-1	luminal epithelium:	n/a	chr19:55850989-55850998 chr19:55851452-55851461
22	TFAP2C	chr19:55850004-55853125	Hela-S3	cervix:	n/a	chr19:55852681-55852696
23	EP300	chr19:55850134-55851226	GM12878	blood:	n/a	chr19:55851210-55851226
24	MAX	chr19:55850058-55851399	K562	blood:	n/a	chr19:55850989-55850998
25	RCOR1	chr19:55850340-55851317	GM12878	blood:	n/a	n/a
26	CTCF	chr19:55850660-55850810	HBMEC	blood vessel:	n/a	n/a
27	MYC	chr19:55850749-55850906	GM12878	blood:	n/a	n/a
28	CTCF	chr19:55850680-55850830	HepG2	liver:	n/a	n/a
29	CUX1	chr19:55850618-55851099	GM12878	blood:	n/a	n/a
30	FOXA2	chr19:55849985-55851345	A549	lung:	n/a	n/a
31	PBX3	chr19:55849882-55851551	SK-N-SH	brain:	n/a	chr19:55851125-55851134 chr19:55851163-55851183 chr19:55850787-55850807 chr19:55850938-55850947 chr19:55850923-55850943
32	MXI1	chr19:55849731-55853168	SK-N-SH	brain:	n/a	chr19:55850630-55850645 chr19:55850628-55850643
33	REST	chr19:55849678-55852977	H1-neurons	neurons:	n/a	chr19:55850854-55850867 chr19:55852837-55852857 chr19:55852394-55852407 chr19:55852837-55852857 chr19:55850816-55850825 chr19:55852837-55852857 chr19:55852179-55852192 chr19:55852840-55852853
34	POLR2A	chr19:55850718-55852051	HCT-116	colon:	n/a	n/a
35	CREB1	chr19:55849965-55851771	K562	blood:	n/a	n/a
36	SP1	chr19:55850383-55851361	GM12878	blood:	n/a	chr19:55850702-55850715 chr19:55851059-55851069 chr19:55851123-55851144 chr19:55850654-55850665 chr19:55850566-55850580 chr19:55851058-55851070 chr19:55851058-55851070 chr19:55851176-55851197 chr19:55851059-55851069
37	RFX5	chr19:55849820-55851612	SK-N-SH	brain:	n/a	chr19:55850988-55851003 chr19:55850628-55850645 chr19:55850629-55850644 chr19:55850938-55850947 chr19:55850629-55850644 chr19:55851146-55851160 chr19:55850629-55850644
38	CEBPB	chr19:55849868-55851369	A549	lung:	n/a	n/a
39	MAX	chr19:55850033-55851413	HepG2	liver:	n/a	chr19:55850989-55850998
40	GATA3	chr19:55849697-55851574	A549	lung:	n/a	n/a
41	POLR2A	chr19:55850443-55851728	MCF-7	breast:	n/a	n/a
42	FOS	chr19:55850067-55851329	Hela-S3	cervix:	n/a	chr19:55850654-55850663 chr19:55851126-55851135
43	MYC	chr19:55849999-55851718	K562	blood:	n/a	chr19:55850989-55850998 chr19:55851452-55851461
44	CTCF	chr19:55850700-55850850	AoAF	blood vessel:	n/a	n/a
45	GATA3	chr19:55849844-55851424	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr19:55850476-55851938	GM12878	blood:	n/a	n/a
47	RELA	chr19:55850136-55851259	GM15510	blood:	n/a	n/a
48	CTCF	chr19:55850516-55851000	K562	blood:	n/a	n/a
49	CTCF	chr19:55850700-55850850	AG10803	skin:	n/a	n/a
50	RFX5	chr19:55850519-55851324	GM12878	blood:	n/a	chr19:55850988-55851003 chr19:55850628-55850645 chr19:55850629-55850644 chr19:55850938-55850947 chr19:55850629-55850644 chr19:55851146-55851160 chr19:55850629-55850644

No.	Distal block	Cell Line	Cell type
1	chr19:55834572..55838662-chr19:55847214..55851799,6	K562	blood:
2	chr19:55812251..55815650-chr19:55848570..55851424,4	MCF-7	breast:
3	chr19:55850053..55852875-chr19:55917610..55920825,5	MCF-7	breast:
4	chr19:55770686..55772282-chr19:55848676..55850979,2	K562	blood:
5	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
6	chr19:55848855..55851022-chr19:55968607..55971004,2	MCF-7	breast:
7	chr19:55788649..55794261-chr19:55847636..55852828,10	K562	blood:
8	chr19:55834572..55838022-chr19:55847724..55851799,4	K562	blood:
9	chr19:55850159..55852267-chr19:56116484..56118952,2	MCF-7	breast:
10	chr19:55847527..55853936-chr19:55895162..55898950,13	K562	blood:
11	chr19:55849062..55852611-chr19:55879307..55883496,5	MCF-7	breast:
12	chr19:55790045..55791863-chr19:55848758..55853021,3	MCF-7	breast:
13	chr19:55813052..55817410-chr19:55850511..55853343,6	MCF-7	breast:
14	chr19:55789812..55792675-chr19:55848548..55852419,5	K562	blood:
15	chr19:55849530..55854944-chr19:55915448..55920939,7	K562	blood:
16	chr19:55849599..55852921-chr19:55970880..55974521,5	K562	blood:
17	chr19:55815976..55818452-chr19:55849117..55850810,2	MCF-7	breast:
18	chr19:55848915..55854876-chr19:55892600..55899757,13	MCF-7	breast:
19	chr19:55847613..55856135-chr19:55893756..55900268,15	K562	blood:

Variant related genes	Relation type
ENSG00000267531	TF binding region
SUV420H2	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000180061	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000160469	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10416740	0.96[EUR][1000 genomes]
rs11879143	0.96[EUR][1000 genomes]
rs12609926	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58051372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59493644	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59695872	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59944279	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73605199	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73605200	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73605202	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73607003	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73607005	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73607008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73607019	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73607024	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats 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	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription 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	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	esv1796007	chr19:55850269-55851289	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
13	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
14	esv20612	chr19:55850619-55851369	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
15	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 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	chr19:55849800-55851600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:55849800-55851600	Active TSS	Fetal Brain Female	brain
3	chr19:55849800-55851800	Active TSS	Brain Germinal Matrix	brain
4	chr19:55849800-55851800	Active TSS	Brain Hippocampus Middle	brain
5	chr19:55849800-55852800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:55849800-55852800	Active TSS	A549	lung
7	chr19:55849800-55853000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:55850000-55850800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:55850000-55850800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:55850000-55850800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:55850000-55850800	Flanking Active TSS	Placenta	Placenta
12	chr19:55850000-55851600	Active TSS	Esophagus	oesophagus
13	chr19:55850000-55851800	Active TSS	Brain Angular Gyrus	brain
14	chr19:55850000-55852000	Active TSS	Thymus	Thymus
15	chr19:55850000-55852200	Active TSS	Left Ventricle	heart
16	chr19:55850000-55852400	Active TSS	Aorta	Aorta
17	chr19:55850000-55852800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:55850000-55852800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:55850000-55852800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:55850000-55853200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr19:55850200-55850800	Active TSS	Right Atrium	heart
22	chr19:55850200-55851400	Active TSS	Primary B cells from cord blood	blood
23	chr19:55850200-55851600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:55850200-55851600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:55850200-55851600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:55850200-55851600	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr19:55850200-55851800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:55850200-55851800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr19:55850200-55851800	Active TSS	Psoas Muscle	Psoas
30	chr19:55850200-55852000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:55850200-55852000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:55850200-55852800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr19:55850200-55852800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr19:55850200-55852800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:55850200-55852800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr19:55850200-55852800	Active TSS	Fetal Kidney	kidney
37	chr19:55850200-55852800	Active TSS	Ovary	ovary
38	chr19:55850400-55851200	Weak transcription	Lung	lung
39	chr19:55850400-55851400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:55850400-55851400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:55850400-55851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:55850400-55851600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:55850400-55851600	Active TSS	Primary T cells from cord blood	blood
44	chr19:55850400-55851600	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:55850400-55851600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr19:55850400-55851600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr19:55850400-55851600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:55850400-55851600	Active TSS	Fetal Intestine Large	intestine
49	chr19:55850400-55851600	Active TSS	Fetal Stomach	stomach
50	chr19:55850400-55851600	Active TSS	Spleen	Spleen

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