Variant report

Variant	rs4072920
Chromosome Location	chr19:55770488-55770489
allele	A/C
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	chr19:55769871-55771537	GM12892	blood:	n/a	n/a
2	EP300	chr19:55770056-55771101	HepG2	liver:	n/a	chr19:55770440-55770456 chr19:55770322-55770338
3	POLR2A	chr19:55770059-55771242	HUVEC	blood vessel:	n/a	n/a
4	TAF1	chr19:55770071-55771054	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF7	chr19:55770094-55771025	H1-hESC	embryonic stem cell:	n/a	n/a
6	RELA	chr19:55770152-55771055	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:55769976-55771235	PBDE	blood:	n/a	n/a
8	POLR2A	chr19:55769949-55771495	K562	blood:	n/a	n/a
9	EP300	chr19:55770395-55770976	HepG2	liver:	n/a	chr19:55770440-55770456
10	ELF1	chr19:55770115-55771182	MCF-7	breast:	n/a	chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770333-55770345
11	UBTF	chr19:55768656-55771041	K562	blood:	n/a	n/a
12	POLR2A	chr19:55769936-55771536	U87	brain:	n/a	n/a
13	SIN3AK20	chr19:55768209-55771137	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:55769829-55771415	GM19099	blood:	n/a	n/a
15	MAFK	chr19:55770447-55771076	K562	blood:	n/a	n/a
16	CHD1	chr19:55770247-55771301	GM12878	blood:	n/a	chr19:55770450-55770460
17	BHLHE40	chr19:55770275-55770987	HepG2	liver:	n/a	n/a
18	MAX	chr19:55770253-55771032	H1-hESC	embryonic stem cell:	n/a	chr19:55770411-55770421
19	CTBP2	chr19:55770110-55770958	H1-hESC	embryonic stem cell:	n/a	n/a
20	EBF1	chr19:55770236-55770941	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:55770182-55771076	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr19:55770269-55770915	GM12878	blood:	n/a	chr19:55770412-55770422 chr19:55770505-55770512 chr19:55770502-55770516 chr19:55770448-55770458 chr19:55770480-55770489 chr19:55770467-55770474 chr19:55770537-55770546 chr19:55770519-55770533 chr19:55770505-55770518
23	JUND	chr19:55770310-55771178	SK-N-SH	brain:	n/a	chr19:55770747-55770761 chr19:55770448-55770457 chr19:55770639-55770653
24	POLR2A	chr19:55769721-55771109	GM18526	blood:	n/a	n/a
25	FOXA2	chr19:55770423-55770821	HepG2	liver:	n/a	n/a
26	PML	chr19:55770109-55771081	MCF-7	breast:	n/a	n/a
27	USF1	chr19:55770127-55771054	A549	lung:	n/a	n/a
28	POLR2A	chr19:55770253-55771060	HepG2	liver:	n/a	n/a
29	ELF1	chr19:55770461-55771097	A549	lung:	n/a	n/a
30	FOS	chr19:55770361-55771006	HUVEC	blood vessel:	n/a	chr19:55770747-55770761 chr19:55770448-55770457 chr19:55770639-55770653
31	POLR2A	chr19:55770078-55771230	U87	brain:	n/a	n/a
32	SIN3AK20	chr19:55770111-55771266	MCF-7	breast:	n/a	n/a
33	ATF3	chr19:55770222-55770967	K562	blood:	n/a	chr19:55770449-55770458
34	POLR2A	chr19:55770098-55771252	GM12878	blood:	n/a	n/a
35	PBX3	chr19:55769993-55771121	SK-N-SH	brain:	n/a	n/a
36	EP300	chr19:55770213-55771160	SK-N-SH	brain:	n/a	chr19:55770440-55770456 chr19:55770322-55770338
37	REST	chr19:55769162-55771383	H1-neurons	neurons:	n/a	chr19:55769581-55769594 chr19:55769348-55769368
38	POLR2A	chr19:55769961-55771209	MCF10A-Er-Src	breast:	n/a	n/a
39	POU2F2	chr19:55770083-55771061	GM12891	blood:	n/a	chr19:55770443-55770455 chr19:55770446-55770458 chr19:55770440-55770452
40	SPI1	chr19:55770017-55771115	HL-60	blood:	n/a	n/a
41	POLR2A	chr19:55769880-55771250	K562	blood:	n/a	n/a
42	SP1	chr19:55770047-55771156	H1-hESC	embryonic stem cell:	n/a	chr19:55770448-55770460 chr19:55770410-55770422 chr19:55770450-55770459 chr19:55770449-55770458 chr19:55770411-55770420 chr19:55770445-55770459 chr19:55770449-55770459 chr19:55770411-55770425 chr19:55770448-55770460 chr19:55770450-55770459 chr19:55770449-55770459 chr19:55770410-55770422 chr19:55770411-55770421 chr19:55770412-55770421
43	PML	chr19:55770051-55771129	K562	blood:	n/a	n/a
44	CTCF	chr19:55770480-55770630	HepG2	liver:	n/a	n/a
45	ZEB1	chr19:55770016-55770948	GM12878	blood:	n/a	chr19:55770440-55770449 chr19:55770438-55770449 chr19:55770437-55770449
46	ZNF143	chr19:55770213-55770918	K562	blood:	n/a	chr19:55770347-55770365 chr19:55770375-55770390
47	GATA3	chr19:55770326-55771004	MCF-7	breast:	n/a	chr19:55770377-55770390
48	TEAD4	chr19:55770146-55771005	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr19:55769907-55771115	ProgFib	skin:	n/a	n/a
50	ELF1	chr19:55770036-55771138	MCF-7	breast:	n/a	chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770073-55770085 chr19:55770333-55770345

No.	Distal block	Cell Line	Cell type
1	chr19:55769670..55772442-chr19:55857047..55859778,2	K562	blood:
2	chr19:55770065..55771348-chr6:146056333..146057332,3	Hela-S3	cervix:
3	chr19:55769985..55770876-chr8:66754056..66754841,2	Hela-S3	cervix:
4	chr19:55769482..55772014-chr19:55910008..55913343,3	K562	blood:
5	chr19:55768392..55770990-chr19:55864103..55865699,2	MCF-7	breast:
6	chr19:55770321..55771177-chr5:39074454..39075248,2	Hela-S3	cervix:
7	chr19:55718690..55723182-chr19:55767265..55771415,7	MCF-7	breast:
8	chr19:55767441..55773483-chr19:55893952..55900251,14	MCF-7	breast:
9	chr19:55690523..55693470-chr19:55767618..55771014,3	K562	blood:
10	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
11	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
12	chr19:55767441..55772178-chr19:55789060..55793175,7	MCF-7	breast:
13	chr19:55727463..55728040-chr19:55770415..55771027,2	HCT-116	colon:
14	chr19:55659384..55662186-chr19:55768928..55771825,2	K562	blood:
15	chr19:55768870..55771541-chr19:55794018..55795820,2	MCF-7	breast:
16	chr19:55769739..55771684-chr19:55850814..55852866,2	MCF-7	breast:
17	chr19:55727159..55729586-chr19:55769569..55772417,4	MCF-7	breast:
18	chr19:55769552..55771558-chr19:55896824..55899608,3	MCF-7	breast:
19	chr19:55657829..55659690-chr19:55769331..55772164,2	K562	blood:
20	chr19:55766592..55768703-chr19:55769065..55770634,3	K562	blood:
21	chr19:55767517..55772398-chr19:55789828..55793738,15	K562	blood:
22	chr19:55768444..55771983-chr19:55917721..55920953,5	K562	blood:
23	chr19:55724113..55730012-chr19:55766381..55773608,39	K562	blood:
24	chr19:55690189..55693086-chr19:55769247..55770801,2	MCF-7	breast:
25	chr19:55768912..55770529-chr19:55917802..55919631,2	MCF-7	breast:
26	chr19:55736575..55738793-chr19:55769011..55771822,2	MCF-7	breast:
27	chr19:55720878..55730679-chr19:55764402..55774570,47	K562	blood:
28	chr19:55756546..55759225-chr19:55768234..55771187,4	MCF-7	breast:
29	chr19:55769028..55772088-chr19:55788931..55793273,6	MCF-7	breast:
30	chr19:55727366..55728438-chr19:55769798..55771153,4	Hela-S3	cervix:
31	chr19:55768430..55771983-chr19:55917442..55920696,5	K562	blood:
32	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
33	chr19:55684145..55687547-chr19:55770390..55772403,3	K562	blood:
34	chr19:55732279..55738678-chr19:55765531..55770516,7	K562	blood:
35	chr19:55767450..55771021-chr19:55880319..55882334,3	MCF-7	breast:
36	chr19:55726024..55729916-chr19:55768850..55773519,13	MCF-7	breast:
37	chr19:55764275..55774774-chr19:55790059..55800763,24	K562	blood:

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000105048	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000205268	Chromatin interaction
ENSG00000164327	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000269808	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108107	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10403164	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403571	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10412187	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414721	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880758	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880781	0.89[AMR][1000 genomes]
rs12983085	0.87[AMR][1000 genomes]
rs4806656	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806657	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62126354	0.86[AMR][1000 genomes]
rs67351527	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv912454	chr19:55725410-55783552	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr19:55766000-55770600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:55768200-55771000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:55768400-55771400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:55768400-55771800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:55768600-55770800	Active TSS	HSMMtube	muscle
6	chr19:55768600-55771000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:55768600-55771200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:55768600-55771200	Active TSS	Ovary	ovary
9	chr19:55768800-55770800	Active TSS	Fetal Intestine Small	intestine
10	chr19:55768800-55771000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:55768800-55771000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr19:55768800-55771000	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr19:55768800-55771000	Active TSS	Fetal Intestine Large	intestine
14	chr19:55768800-55771000	Active TSS	Small Intestine	intestine
15	chr19:55768800-55771000	Active TSS	Thymus	Thymus
16	chr19:55768800-55771000	Active TSS	A549	lung
17	chr19:55768800-55771000	Active TSS	GM12878-XiMat	blood
18	chr19:55768800-55771000	Active TSS	K562	blood
19	chr19:55768800-55771000	Active TSS	NHLF	lung
20	chr19:55768800-55771200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:55768800-55771200	Active TSS	Esophagus	oesophagus
22	chr19:55768800-55771200	Active TSS	HSMM	muscle
23	chr19:55768800-55771200	Active TSS	NHDF-Ad	bronchial
24	chr19:55768800-55771400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:55768800-55771400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr19:55768800-55771400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr19:55769000-55770800	Active TSS	Fetal Thymus	thymus
28	chr19:55769000-55770800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr19:55769000-55771000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:55769000-55771200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:55769000-55771200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:55769000-55771200	Active TSS	Colon Smooth Muscle	Colon
33	chr19:55769000-55771200	Active TSS	Fetal Kidney	kidney
34	chr19:55769000-55771200	Active TSS	Rectal Smooth Muscle	rectum
35	chr19:55769000-55771200	Active TSS	HepG2	liver
36	chr19:55769000-55771400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:55769000-55771400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:55769000-55771600	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr19:55769200-55770600	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:55769200-55770800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:55769200-55770800	Active TSS	Primary T cells from cord blood	blood
42	chr19:55769200-55770800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:55769200-55770800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr19:55769200-55770800	Active TSS	Fetal Lung	lung
45	chr19:55769200-55770800	Active TSS	Hela-S3	cervix
46	chr19:55769200-55770800	Active TSS	NH-A	brain
47	chr19:55769200-55770800	Active TSS	Osteobl	bone
48	chr19:55769200-55771000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:55769200-55771000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:55769200-55771000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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