Variant report

Variant	rs56849284
Chromosome Location	chr19:38826947-38826948
allele	C/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	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	CTCF	chr19:38825440-38827183	A549	lung:	n/a	chr19:38826291-38826309 chr19:38826985-38826995
6	SP4	chr19:38826703-38827877	H1-hESC	embryonic stem cell:	n/a	chr19:38827423-38827439
7	SIN3AK20	chr19:38825942-38827717	PANC-1	pancreas:	n/a	n/a
8	SRF	chr19:38826931-38827136	GM12878	blood:	n/a	n/a
9	MAX	chr19:38826010-38828085	A549	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
10	POLR2A	chr19:38826192-38828012	HL-60	blood:	n/a	n/a
11	RUNX3	chr19:38826884-38827674	GM12878	blood:	n/a	n/a
12	ELF1	chr19:38826797-38827470	A549	lung:	n/a	n/a
13	RAD21	chr19:38825911-38827976	HCT-116	colon:	n/a	chr19:38826289-38826308 chr19:38826986-38826996 chr19:38826985-38826994
14	SIN3AK20	chr19:38826190-38827745	A549	lung:	n/a	n/a
15	POLR2A	chr19:38826661-38827307	SK-N-SH	brain:	n/a	n/a
16	MAX	chr19:38826165-38827994	NB4	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
17	NFYB	chr19:38826876-38827167	Hela-S3	cervix:	n/a	chr19:38827018-38827033 chr19:38827023-38827033
18	MAX	chr19:38826144-38827956	SK-N-SH	brain:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
19	EP300	chr19:38826161-38827269	K562	blood:	n/a	n/a
20	POLR2A	chr19:38826815-38827276	GM12891	blood:	n/a	n/a
21	CBX3	chr19:38826674-38827845	K562	blood:	n/a	n/a
22	BRCA1	chr19:38826832-38827711	Hela-S3	cervix:	n/a	n/a
23	BACH1	chr19:38826254-38828128	H1-hESC	embryonic stem cell:	n/a	n/a
24	RCOR1	chr19:38826779-38827497	GM12878	blood:	n/a	n/a
25	MAZ	chr19:38826145-38828113	K562	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
26	TBL1XR1	chr19:38826943-38827932	K562	blood:	n/a	n/a
27	REST	chr19:38826514-38826988	A549	lung:	n/a	chr19:38826962-38826975
28	SMC3	chr19:38826927-38827417	GM12878	blood:	n/a	n/a
29	TEAD4	chr19:38826929-38827620	K562	blood:	n/a	n/a
30	MAZ	chr19:38826062-38828017	IMR90	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
31	HDAC2	chr19:38826858-38827670	H1-hESC	embryonic stem cell:	n/a	n/a
32	JUND	chr19:38826937-38827335	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr19:38826816-38827179	A549	lung:	n/a	n/a
34	CHD2	chr19:38826205-38827248	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr19:38826694-38827346	K562	blood:	n/a	n/a
36	NFYA	chr19:38826830-38827202	Hela-S3	cervix:	n/a	chr19:38827023-38827033
37	TBL1XR1	chr19:38826787-38826973	K562	blood:	n/a	n/a
38	POLR2A	chr19:38826169-38827785	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr19:38826751-38827337	A549	lung:	n/a	n/a
40	CHD2	chr19:38826205-38827206	K562	blood:	n/a	n/a
41	ZEB1	chr19:38826184-38827693	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:38826806-38827224	Hela-S3	cervix:	n/a	n/a
43	CREB1	chr19:38826051-38827921	GM12878	blood:	n/a	n/a
44	BHLHE40	chr19:38826202-38827404	HepG2	liver:	n/a	chr19:38827084-38827100
45	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
46	CTCF	chr19:38826855-38826979	GM12878	blood:	n/a	n/a
47	YY1	chr19:38826720-38827260	SK-N-SH_RA	brain:	n/a	n/a
48	ETS1	chr19:38826198-38826961	A549	lung:	n/a	n/a
49	RFX5	chr19:38826762-38827582	GM12878	blood:	n/a	n/a
50	MXI1	chr19:38826213-38826987	H1-hESC	embryonic stem cell:	n/a	chr19:38826368-38826383

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	chr19:38826766..38829028-chr19:38851929..38854753,2	K562	blood:
29	chr19:38826901..38827604-chr19:38865042..38865625,2	Hela-S3	cervix:
30	chr19:38810007..38812286-chr19:38825422..38828123,4	MCF-7	breast:
31	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:

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

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12609247	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12611255	0.90[EUR][1000 genomes]
rs2270095	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286475	0.91[EUR][1000 genomes]
rs2286476	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304176	0.88[EUR][1000 genomes]
rs3815345	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57618695	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58728151	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59898212	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60071299	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61160177	0.93[EUR][1000 genomes]
rs7252835	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253960	0.93[EUR][1000 genomes]
rs73043010	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73043037	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112211	0.81[AMR][1000 genomes];0.99[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	chr19:38826000-38827200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:38826000-38827200	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr19:38826000-38827200	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:38826000-38827800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:38826000-38827800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:38826000-38827800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38826000-38827800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:38826000-38827800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:38826000-38828000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:38826000-38828000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:38826000-38828000	Active TSS	Fetal Brain Female	brain
14	chr19:38826000-38828200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:38826000-38828200	Active TSS	HSMM	muscle
16	chr19:38826200-38827800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:38826200-38827800	Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr19:38826200-38827800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:38826200-38827800	Active TSS	Thymus	Thymus
20	chr19:38826200-38828000	Active TSS	Fetal Kidney	kidney
21	chr19:38826200-38828200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:38826200-38828200	Active TSS	Brain Anterior Caudate	brain
23	chr19:38826400-38827200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr19:38826400-38827200	Active TSS	Adipose Nuclei	Adipose
25	chr19:38826400-38827200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr19:38826400-38827400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:38826400-38827400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:38826400-38827400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:38826400-38827400	Active TSS	Right Ventricle	heart
30	chr19:38826400-38827400	Active TSS	NH-A	brain
31	chr19:38826400-38827600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:38826400-38827600	Active TSS	Brain Germinal Matrix	brain
33	chr19:38826400-38827600	Active TSS	Fetal Muscle Leg	muscle
34	chr19:38826400-38827600	Active TSS	Fetal Stomach	stomach
35	chr19:38826400-38827600	Flanking Active TSS	Dnd41	blood
36	chr19:38826400-38827800	Active TSS	H1 Cell Line	embryonic stem cell
37	chr19:38826400-38827800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38826400-38827800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr19:38826400-38827800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:38826400-38827800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38826400-38827800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:38826400-38827800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr19:38826400-38827800	Active TSS	Primary B cells from peripheral blood	blood
44	chr19:38826400-38827800	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:38826400-38827800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:38826400-38827800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr19:38826400-38827800	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr19:38826400-38827800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:38826400-38827800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:38826400-38827800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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