Variant report

Variant	rs73043013
Chromosome Location	chr19:38827568-38827569
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	chr19:38826201-38827970	MCF10A-Er-Src	breast:	n/a	n/a
2	GABPA	chr19:38826207-38827798	SK-N-SH	brain:	n/a	chr19:38826312-38826321
3	POLR2A	chr19:38826619-38827969	PFSK-1	brain:	n/a	n/a
4	YY1	chr19:38826095-38828043	A549	lung:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448 chr19:38827480-38827489
5	SP4	chr19:38826703-38827877	H1-hESC	embryonic stem cell:	n/a	chr19:38827423-38827439
6	SIN3AK20	chr19:38825942-38827717	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:38827313-38827973	HCT-116	colon:	n/a	n/a
8	MAX	chr19:38826010-38828085	A549	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
9	POLR2A	chr19:38826192-38828012	HL-60	blood:	n/a	n/a
10	RUNX3	chr19:38826884-38827674	GM12878	blood:	n/a	n/a
11	RAD21	chr19:38825911-38827976	HCT-116	colon:	n/a	chr19:38826289-38826308 chr19:38826986-38826996 chr19:38826985-38826994
12	SIN3AK20	chr19:38826190-38827745	A549	lung:	n/a	n/a
13	MAX	chr19:38826165-38827994	NB4	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
14	POLR2A	chr19:38827301-38827735	K562	blood:	n/a	n/a
15	RCOR1	chr19:38827513-38827948	Hela-S3	cervix:	n/a	n/a
16	MAX	chr19:38826144-38827956	SK-N-SH	brain:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
17	FOXP2	chr19:38827435-38827742	SK-N-MC	brain:	n/a	n/a
18	CBX3	chr19:38826674-38827845	K562	blood:	n/a	n/a
19	BRCA1	chr19:38826832-38827711	Hela-S3	cervix:	n/a	n/a
20	BACH1	chr19:38826254-38828128	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAZ	chr19:38826145-38828113	K562	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
22	TBL1XR1	chr19:38826943-38827932	K562	blood:	n/a	n/a
23	NFIC	chr19:38827228-38827646	GM12878	blood:	n/a	n/a
24	TEAD4	chr19:38826929-38827620	K562	blood:	n/a	n/a
25	MAZ	chr19:38826062-38828017	IMR90	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
26	HDAC2	chr19:38826858-38827670	H1-hESC	embryonic stem cell:	n/a	n/a
27	BRCA1	chr19:38827565-38828013	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:38827553-38827696	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr19:38827162-38828248	A549	lung:	n/a	n/a
30	POLR2A	chr19:38826169-38827785	PANC-1	pancreas:	n/a	n/a
31	E2F6	chr19:38827220-38828045	A549	lung:	n/a	chr19:38827480-38827489
32	ZEB1	chr19:38826184-38827693	GM12878	blood:	n/a	n/a
33	CREB1	chr19:38826051-38827921	GM12878	blood:	n/a	n/a
34	RFX5	chr19:38826762-38827582	GM12878	blood:	n/a	n/a
35	MYC	chr19:38827447-38827864	MCF10A-Er-Src	breast:	n/a	chr19:38827478-38827488
36	POLR2A	chr19:38826188-38828058	Raji	blood:	n/a	n/a
37	MAZ	chr19:38826158-38827894	GM12878	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
38	MAX	chr19:38827337-38828089	H1-hESC	embryonic stem cell:	n/a	chr19:38827422-38827432 chr19:38827478-38827488
39	MXI1	chr19:38825930-38828215	SK-N-SH	brain:	n/a	chr19:38826368-38826383
40	RFX5	chr19:38827484-38827721	Hela-S3	cervix:	n/a	n/a
41	EGR1	chr19:38827262-38827991	K562	blood:	n/a	chr19:38827423-38827436 chr19:38827425-38827435 chr19:38827480-38827490 chr19:38827673-38827687 chr19:38827477-38827487 chr19:38827721-38827735 chr19:38827423-38827436 chr19:38827422-38827437 chr19:38827697-38827711
42	JUN	chr19:38826099-38828496	K562	blood:	n/a	n/a
43	SIN3AK20	chr19:38826154-38827644	A549	lung:	n/a	n/a
44	EGR1	chr19:38826746-38828169	HCT-116	colon:	n/a	chr19:38827423-38827436 chr19:38827425-38827435 chr19:38827480-38827490 chr19:38827673-38827687 chr19:38827477-38827487 chr19:38827721-38827735 chr19:38827423-38827436 chr19:38827422-38827437 chr19:38827697-38827711
45	POLR2A	chr19:38826727-38827886	GM12891	blood:	n/a	n/a
46	YY1	chr19:38826055-38828060	HepG2	liver:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448 chr19:38827480-38827489
47	TEAD4	chr19:38827565-38828282	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr19:38827559-38828133	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr19:38827439-38827605	A549	lung:	n/a	n/a
50	ELF1	chr19:38826007-38827687	GM12878	blood:	n/a	chr19:38826407-38826420 chr19:38826548-38826560 chr19:38826410-38826419

No.	Distal block	Cell Line	Cell type
1	chr19:38804679..38808674-chr19:38824887..38827856,7	K562	blood:
2	chr19:38715608..38719883-chr19:38825304..38828918,6	K562	blood:
3	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
4	chr19:38825004..38828693-chr19:38863595..38867873,9	K562	blood:
5	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
6	chr19:38826968..38827628-chr19:38864752..38865615,2	K562	blood:
7	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
8	chr19:38825537..38827989-chr19:38835886..38838412,2	K562	blood:
9	chr19:38753791..38756428-chr19:38824915..38829046,7	MCF-7	breast:
10	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
11	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
12	chr19:38826223..38828930-chr19:38842574..38845020,2	MCF-7	breast:
13	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
14	chr19:38826489..38830578-chr19:38835148..38838719,4	K562	blood:
15	chr19:38825745..38829204-chr19:38906597..38909224,3	K562	blood:
16	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
17	chr19:38793475..38795482-chr19:38826442..38828638,2	K562	blood:
18	chr19:38733984..38735573-chr19:38825634..38828607,2	K562	blood:
19	chr19:38827274..38829284-chr19:38833779..38835815,2	MCF-7	breast:
20	chr19:38746246..38748291-chr19:38825736..38828521,3	K562	blood:
21	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
22	chr19:38712277..38715341-chr19:38824721..38827828,3	K562	blood:
23	chr19:38777648..38780643-chr19:38825334..38827865,2	K562	blood:
24	chr19:38745286..38748830-chr19:38824490..38828580,5	K562	blood:
25	chr19:38733182..38735640-chr19:38825420..38827758,3	K562	blood:
26	chr19:38825387..38828116-chr19:38877119..38879831,3	MCF-7	breast:
27	chr19:38826766..38829028-chr19:38851929..38854753,2	K562	blood:
28	chr19:38826901..38827604-chr19:38865042..38865625,2	Hela-S3	cervix:
29	chr19:38810007..38812286-chr19:38825422..38828123,4	MCF-7	breast:
30	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000167641	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000167645	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1060454	0.92[ASN][1000 genomes]
rs2270092	1.00[ASN][1000 genomes]
rs2286548	0.92[ASN][1000 genomes]
rs2302185	0.84[ASN][1000 genomes]
rs2302187	0.92[ASN][1000 genomes]
rs3745953	0.92[ASN][1000 genomes]
rs3786881	0.92[ASN][1000 genomes]
rs3786882	0.92[ASN][1000 genomes]
rs3885340	0.87[EUR][1000 genomes]
rs61734615	0.87[EUR][1000 genomes]
rs73037321	0.87[EUR][1000 genomes]
rs73037333	0.84[EUR][1000 genomes]
rs73037343	0.87[EUR][1000 genomes]
rs73037346	0.87[EUR][1000 genomes]
rs73041292	0.87[EUR][1000 genomes]
rs73043012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043019	1.00[EUR][1000 genomes]
rs73043021	1.00[EUR][1000 genomes]
rs73043022	1.00[EUR][1000 genomes]
rs73043027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73043028	1.00[EUR][1000 genomes]
rs73043029	0.97[EUR][1000 genomes]
rs73043030	0.84[EUR][1000 genomes]
rs73043033	0.84[EUR][1000 genomes]
rs73043098	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	esv21001	chr19:38826488-38827974	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 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	chr19:38825600-38827800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:38825800-38827800	Active TSS	Osteobl	bone
3	chr19:38826000-38827800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:38826000-38827800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:38826000-38827800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38826000-38827800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:38826000-38827800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:38826000-38828000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:38826000-38828000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:38826000-38828000	Active TSS	Fetal Brain Female	brain
11	chr19:38826000-38828200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:38826000-38828200	Active TSS	HSMM	muscle
13	chr19:38826200-38827800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:38826200-38827800	Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr19:38826200-38827800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:38826200-38827800	Active TSS	Thymus	Thymus
17	chr19:38826200-38828000	Active TSS	Fetal Kidney	kidney
18	chr19:38826200-38828200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:38826200-38828200	Active TSS	Brain Anterior Caudate	brain
20	chr19:38826400-38827600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:38826400-38827600	Active TSS	Brain Germinal Matrix	brain
22	chr19:38826400-38827600	Active TSS	Fetal Muscle Leg	muscle
23	chr19:38826400-38827600	Active TSS	Fetal Stomach	stomach
24	chr19:38826400-38827600	Flanking Active TSS	Dnd41	blood
25	chr19:38826400-38827800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr19:38826400-38827800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38826400-38827800	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr19:38826400-38827800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:38826400-38827800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:38826400-38827800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:38826400-38827800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:38826400-38827800	Active TSS	Primary B cells from peripheral blood	blood
33	chr19:38826400-38827800	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr19:38826400-38827800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:38826400-38827800	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:38826400-38827800	Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr19:38826400-38827800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:38826400-38827800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr19:38826400-38827800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:38826400-38827800	Active TSS	Brain Angular Gyrus	brain
41	chr19:38826400-38827800	Active TSS	Brain Cingulate Gyrus	brain
42	chr19:38826400-38827800	Active TSS	Brain Hippocampus Middle	brain
43	chr19:38826400-38827800	Active TSS	Colonic Mucosa	Colon
44	chr19:38826400-38827800	Active TSS	Colon Smooth Muscle	Colon
45	chr19:38826400-38827800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr19:38826400-38827800	Active TSS	Fetal Intestine Large	intestine
47	chr19:38826400-38827800	Active TSS	Fetal Intestine Small	intestine
48	chr19:38826400-38827800	Active TSS	Fetal Thymus	thymus
49	chr19:38826400-38827800	Active TSS	Left Ventricle	heart
50	chr19:38826400-38827800	Active TSS	Psoas Muscle	Psoas

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