Variant report

Variant	rs561590098
Chromosome Location	chr19:38826660-38826661
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	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	CTCF	chr19:38826048-38826735	HCT-116	colon:	n/a	chr19:38826291-38826309
5	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
6	CTCF	chr19:38825440-38827183	A549	lung:	n/a	chr19:38826291-38826309 chr19:38826985-38826995
7	SIN3AK20	chr19:38825942-38827717	PANC-1	pancreas:	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	RAD21	chr19:38825911-38827976	HCT-116	colon:	n/a	chr19:38826289-38826308 chr19:38826986-38826996 chr19:38826985-38826994
11	SIN3AK20	chr19:38826190-38827745	A549	lung:	n/a	n/a
12	EBF1	chr19:38826326-38826810	GM12878	blood:	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	MAX	chr19:38826144-38827956	SK-N-SH	brain:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
15	EP300	chr19:38826161-38827269	K562	blood:	n/a	n/a
16	BACH1	chr19:38826254-38828128	H1-hESC	embryonic stem cell:	n/a	n/a
17	GABPA	chr19:38826078-38826665	A549	lung:	n/a	chr19:38826312-38826321
18	MAZ	chr19:38826145-38828113	K562	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
19	REST	chr19:38826514-38826988	A549	lung:	n/a	chr19:38826962-38826975
20	MAZ	chr19:38826062-38828017	IMR90	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
21	CHD2	chr19:38826205-38827248	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:38826169-38827785	PANC-1	pancreas:	n/a	n/a
23	CHD2	chr19:38826205-38827206	K562	blood:	n/a	n/a
24	ZEB1	chr19:38826184-38827693	GM12878	blood:	n/a	n/a
25	CREB1	chr19:38826051-38827921	GM12878	blood:	n/a	n/a
26	BHLHE40	chr19:38826202-38827404	HepG2	liver:	n/a	chr19:38827084-38827100
27	YY1	chr19:38826106-38827240	GM12878	blood:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448
28	CREB1	chr19:38826154-38826703	HepG2	liver:	n/a	n/a
29	ETS1	chr19:38826198-38826961	A549	lung:	n/a	n/a
30	MXI1	chr19:38826213-38826987	H1-hESC	embryonic stem cell:	n/a	chr19:38826368-38826383
31	EP300	chr19:38826102-38826789	A549	lung:	n/a	n/a
32	POLR2A	chr19:38826188-38828058	Raji	blood:	n/a	n/a
33	MAZ	chr19:38826158-38827894	GM12878	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
34	MXI1	chr19:38825930-38828215	SK-N-SH	brain:	n/a	chr19:38826368-38826383
35	JUN	chr19:38826099-38828496	K562	blood:	n/a	n/a
36	SIN3AK20	chr19:38826154-38827644	A549	lung:	n/a	n/a
37	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
38	USF1	chr19:38826147-38826697	ECC-1	luminal epithelium:	n/a	n/a
39	ELF1	chr19:38826007-38827687	GM12878	blood:	n/a	chr19:38826407-38826420 chr19:38826548-38826560 chr19:38826410-38826419
40	MAX	chr19:38826056-38828269	ECC-1	luminal epithelium:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
41	YY1	chr19:38826198-38827351	ECC-1	luminal epithelium:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448
42	MYC	chr19:38826145-38827970	NB4	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
43	BCL3	chr19:38826097-38827124	A549	lung:	n/a	chr19:38826551-38826560
44	TCF12	chr19:38826177-38826905	A549	lung:	n/a	n/a
45	YY1	chr19:38826103-38826671	K562	blood:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448
46	SIN3AK20	chr19:38826192-38827672	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD1	chr19:38826057-38828015	IMR90	lung:	n/a	n/a
48	TAF1	chr19:38826219-38827311	H1-neurons	neurons:	n/a	n/a
49	TCF12	chr19:38825692-38828079	A549	lung:	n/a	n/a
50	REST	chr19:38826039-38827907	A549	lung:	n/a	chr19:38826371-38826380 chr19:38826290-38826303 chr19:38827441-38827454 chr19:38826962-38826975

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	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
7	chr19:38825537..38827989-chr19:38835886..38838412,2	K562	blood:
8	chr19:38753791..38756428-chr19:38824915..38829046,7	MCF-7	breast:
9	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
10	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
11	chr19:38826223..38828930-chr19:38842574..38845020,2	MCF-7	breast:
12	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
13	chr19:38826489..38830578-chr19:38835148..38838719,4	K562	blood:
14	chr19:38825745..38829204-chr19:38906597..38909224,3	K562	blood:
15	chr19:38826520..38827474-chr7:66146585..66147505,2	Hela-S3	cervix:
16	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
17	chr19:38793475..38795482-chr19:38826442..38828638,2	K562	blood:
18	chr19:38733321..38734847-chr19:38824832..38827411,2	MCF-7	breast:
19	chr19:38733984..38735573-chr19:38825634..38828607,2	K562	blood:
20	chr19:38741131..38744022-chr19:38825237..38827049,2	K562	blood:
21	chr19:38746246..38748291-chr19:38825736..38828521,3	K562	blood:
22	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
23	chr19:38712277..38715341-chr19:38824721..38827828,3	K562	blood:
24	chr19:38777648..38780643-chr19:38825334..38827865,2	K562	blood:
25	chr19:38745286..38748830-chr19:38824490..38828580,5	K562	blood:
26	chr19:38733182..38735640-chr19:38825420..38827758,3	K562	blood:
27	chr19:38825387..38828116-chr19:38877119..38879831,3	MCF-7	breast:
28	chr19:38810007..38812286-chr19:38825422..38828123,4	MCF-7	breast:
29	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000011332	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	chr19:38813200-38826800	Weak transcription	Fetal Heart	heart
2	chr19:38825600-38827800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:38825800-38827800	Active TSS	Osteobl	bone
4	chr19:38826000-38827200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:38826000-38827200	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr19:38826000-38827200	Active TSS	Stomach Smooth Muscle	stomach
7	chr19:38826000-38827800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:38826000-38827800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:38826000-38827800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38826000-38827800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:38826000-38827800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:38826000-38828000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:38826000-38828000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:38826000-38828000	Active TSS	Fetal Brain Female	brain
15	chr19:38826000-38828200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:38826000-38828200	Active TSS	HSMM	muscle
17	chr19:38826200-38826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:38826200-38826800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:38826200-38827800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:38826200-38827800	Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr19:38826200-38827800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:38826200-38827800	Active TSS	Thymus	Thymus
23	chr19:38826200-38828000	Active TSS	Fetal Kidney	kidney
24	chr19:38826200-38828200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:38826200-38828200	Active TSS	Brain Anterior Caudate	brain
26	chr19:38826400-38826800	Active TSS	Primary hematopoietic stem cells	blood
27	chr19:38826400-38826800	Transcr. at gene 5' and 3'	Right Atrium	heart
28	chr19:38826400-38826800	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr19:38826400-38827200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr19:38826400-38827200	Active TSS	Adipose Nuclei	Adipose
31	chr19:38826400-38827200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr19:38826400-38827400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:38826400-38827400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:38826400-38827400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr19:38826400-38827400	Active TSS	Right Ventricle	heart
36	chr19:38826400-38827400	Active TSS	NH-A	brain
37	chr19:38826400-38827600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:38826400-38827600	Active TSS	Brain Germinal Matrix	brain
39	chr19:38826400-38827600	Active TSS	Fetal Muscle Leg	muscle
40	chr19:38826400-38827600	Active TSS	Fetal Stomach	stomach
41	chr19:38826400-38827600	Flanking Active TSS	Dnd41	blood
42	chr19:38826400-38827800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr19:38826400-38827800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:38826400-38827800	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:38826400-38827800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:38826400-38827800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:38826400-38827800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:38826400-38827800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr19:38826400-38827800	Active TSS	Primary B cells from peripheral blood	blood
50	chr19:38826400-38827800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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