Variant report

Variant	rs550545910
Chromosome Location	chr19:19516233-19516234
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	RUNX3	chr19:19515881-19516660	GM12878	blood:	n/a	n/a
2	USF2	chr19:19515874-19516462	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr19:19515685-19518134	MCF-7	breast:	n/a	n/a
4	BCL3	chr19:19516095-19516470	GM12878	blood:	n/a	n/a
5	CTCF	chr19:19516180-19516330	HEK293	kidney:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
6	CTCF	chr19:19516100-19516250	HFF-Myc	foreskin:	n/a	n/a
7	POLR2A	chr19:19515960-19516750	Hela-S3	cervix:	n/a	n/a
8	HA-E2F1	chr19:19515978-19517416	Hela-S3	cervix:	n/a	chr19:19516853-19516862 chr19:19516596-19516606 chr19:19516392-19516401 chr19:19516857-19516867 chr19:19517170-19517182 chr19:19516597-19516607
9	EP300	chr19:19516181-19516433	HepG2	liver:	n/a	n/a
10	CHD2	chr19:19516088-19516496	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:19516102-19516792	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:19516095-19516830	GM12892	blood:	n/a	n/a
13	NFIC	chr19:19515851-19516259	GM12878	blood:	n/a	n/a
14	MAX	chr19:19515608-19517578	A549	lung:	n/a	chr19:19517185-19517192 chr19:19517317-19517326 chr19:19517183-19517194 chr19:19517184-19517193 chr19:19517184-19517194 chr19:19517168-19517178 chr19:19516393-19516403 chr19:19517041-19517050 chr19:19517043-19517052 chr19:19517042-19517049 chr19:19517186-19517195
15	ELF1	chr19:19515973-19516646	K562	blood:	n/a	n/a
16	SIN3AK20	chr19:19516085-19516747	PANC-1	pancreas:	n/a	n/a
17	RAD21	chr19:19515986-19516486	ECC-1	luminal epithelium:	n/a	chr19:19516260-19516274 chr19:19516264-19516276 chr19:19516259-19516278
18	CTCF	chr19:19516180-19516330	K562	blood:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
19	MAFK	chr19:19516027-19516470	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr19:19516089-19516437	HepG2	liver:	n/a	chr19:19516260-19516274 chr19:19516264-19516276 chr19:19516259-19516278
21	MAX	chr19:19516019-19516610	K562	blood:	n/a	chr19:19516393-19516403
22	POLR2A	chr19:19515979-19516978	MCF-7	breast:	n/a	n/a
23	MAZ	chr19:19515842-19516724	GM12878	blood:	n/a	chr19:19516393-19516403
24	CTCF	chr19:19516180-19516330	GM12869	blood:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
25	MYC	chr19:19516062-19516380	MCF-7	breast:	n/a	n/a
26	TEAD4	chr19:19515691-19516511	K562	blood:	n/a	n/a
27	MXI1	chr19:19515852-19516655	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:19515983-19516363	Hela-S3	cervix:	n/a	n/a
29	GABPA	chr19:19516031-19516575	MCF-7	breast:	n/a	chr19:19516434-19516443 chr19:19516392-19516401
30	POLR2A	chr19:19515844-19516451	U87	brain:	n/a	n/a
31	ELF1	chr19:19515927-19516552	HepG2	liver:	n/a	n/a
32	SIN3AK20	chr19:19516008-19516525	SK-N-SH	brain:	n/a	n/a
33	TCF12	chr19:19515867-19516532	ECC-1	luminal epithelium:	n/a	chr19:19516166-19516173
34	CTCF	chr19:19516121-19516386	NHEK	skin:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
35	CTCF	chr19:19516160-19516310	GM12864	blood:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
36	POLR2A	chr19:19515949-19516729	K562	blood:	n/a	n/a
37	SIN3A	chr19:19515904-19516591	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:19516186-19516278	HepG2	liver:	n/a	n/a
39	REST	chr19:19516149-19516637	PFSK-1	brain:	n/a	n/a
40	GABPA	chr19:19516114-19516493	HepG2	liver:	n/a	chr19:19516434-19516443 chr19:19516392-19516401
41	POLR2A	chr19:19515990-19516675	GM12878	blood:	n/a	n/a
42	EGR1	chr19:19515958-19516688	HCT-116	colon:	n/a	chr19:19516039-19516049 chr19:19516391-19516401 chr19:19516390-19516404 chr19:19516392-19516407 chr19:19516393-19516406 chr19:19516393-19516406 chr19:19516393-19516406 chr19:19516103-19516112
43	CTCF	chr19:19516180-19516330	HepG2	liver:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
44	TBP	chr19:19516150-19516569	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:19516088-19516750	H1-neurons	neurons:	n/a	n/a
46	TCF12	chr19:19515880-19516645	A549	lung:	n/a	chr19:19516166-19516173
47	CTCF	chr19:19516160-19516310	HRPEpiC	eye:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
48	POLR2A	chr19:19515971-19516837	HL-60	blood:	n/a	n/a
49	CTCF	chr19:19516160-19516310	AG09319	gingival:	n/a	chr19:19516261-19516274 chr19:19516258-19516276
50	CTCF	chr19:19516140-19516290	HA-sp	spinal cord:	n/a	chr19:19516261-19516274 chr19:19516258-19516276

No.	Distal block	Cell Line	Cell type
1	chr19:19515119..19517741-chr19:19568755..19571176,2	MCF-7	breast:
2	chr19:19496016..19496749-chr19:19516167..19516951,2	K562	blood:
3	chr19:19028947..19031173-chr19:19514626..19517474,2	K562	blood:
4	chr19:19515140..19518800-chr19:19574675..19578008,3	K562	blood:
5	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
6	chr19:19514082..19516953-chr19:19567668..19570496,2	K562	blood:
7	chr19:19514894..19516950-chr19:19536458..19538380,2	MCF-7	breast:
8	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
9	chr19:19516170..19518046-chr20:30944497..30946734,2	K562	blood:
10	chr19:19428553..19432587-chr19:19515649..19520173,6	K562	blood:
11	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:
12	chr12:122985085..122985747-chr19:19516157..19516988,2	Hela-S3	cervix:
13	chr19:19494732..19500297-chr19:19512585..19520288,14	MCF-7	breast:
14	chr19:19454032..19456725-chr19:19515938..19518682,3	K562	blood:
15	chr19:19514840..19518062-chr19:19543803..19546421,4	K562	blood:
16	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000267234	TF binding region
ENSG00000167491	Chromatin interaction
ENSG00000171456	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000207821	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000105671	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv3360569	chr19:19515477-19518325	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3411112	chr19:19515802-19518225	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	9 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	chr19:19515400-19516400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr19:19515400-19517600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:19515600-19516400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:19515600-19517600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:19515600-19517600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:19515600-19517800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:19515600-19517800	Active TSS	Colon Smooth Muscle	Colon
8	chr19:19515600-19517800	Active TSS	Fetal Kidney	kidney
9	chr19:19515600-19518000	Active TSS	Brain Anterior Caudate	brain
10	chr19:19515600-19518200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:19515800-19516400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:19515800-19516400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:19515800-19516400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr19:19515800-19516400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr19:19515800-19516400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:19515800-19516400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:19515800-19516400	Flanking Active TSS	Pancreas	Pancrea
18	chr19:19515800-19516400	Flanking Active TSS	Dnd41	blood
19	chr19:19515800-19516400	Flanking Active TSS	NH-A	brain
20	chr19:19515800-19517400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19515800-19517400	Active TSS	Brain Angular Gyrus	brain
22	chr19:19515800-19517400	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr19:19515800-19517600	Active TSS	Brain Germinal Matrix	brain
24	chr19:19515800-19517600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:19515800-19517600	Active TSS	Fetal Stomach	stomach
26	chr19:19515800-19518000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:19515800-19518000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr19:19515800-19518000	Active TSS	Aorta	Aorta
29	chr19:19515800-19518000	Active TSS	Gastric	stomach
30	chr19:19515800-19518200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr19:19515800-19518200	Active TSS	Ovary	ovary
32	chr19:19515800-19518200	Active TSS	Psoas Muscle	Psoas
33	chr19:19515800-19518800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:19516000-19516400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:19516000-19516400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr19:19516000-19516400	Active TSS	Fetal Brain Male	brain
37	chr19:19516000-19517400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr19:19516000-19517400	Active TSS	Brain Hippocampus Middle	brain
39	chr19:19516000-19517400	Weak transcription	Fetal Heart	heart
40	chr19:19516000-19517600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr19:19516000-19517600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr19:19516000-19517600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:19516000-19517600	Active TSS	Brain Substantia Nigra	brain
44	chr19:19516000-19517600	Active TSS	Duodenum Mucosa	Duodenum
45	chr19:19516000-19517600	Active TSS	Fetal Brain Female	brain
46	chr19:19516000-19517600	Active TSS	Fetal Lung	lung
47	chr19:19516000-19517600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr19:19516000-19517600	Active TSS	Rectal Smooth Muscle	rectum
49	chr19:19516000-19517600	Active TSS	HSMM	muscle
50	chr19:19516000-19517600	Active TSS	NHDF-Ad	bronchial

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