Variant report

Variant	rs542015909
Chromosome Location	chr19:19516677-19516678
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	SIN3AK20	chr19:19515685-19518134	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:19515960-19516750	Hela-S3	cervix:	n/a	n/a
3	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
4	POLR2A	chr19:19516102-19516792	GM12878	blood:	n/a	n/a
5	EGR1	chr19:19516288-19516692	H1-hESC	embryonic stem cell:	n/a	chr19:19516391-19516401 chr19:19516390-19516404 chr19:19516392-19516407 chr19:19516393-19516406 chr19:19516393-19516406 chr19:19516393-19516406
6	POLR2A	chr19:19516095-19516830	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:19516392-19516995	K562	blood:	n/a	n/a
8	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
9	TAF1	chr19:19516486-19516678	GM12891	blood:	n/a	n/a
10	SIN3AK20	chr19:19516085-19516747	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:19515979-19516978	MCF-7	breast:	n/a	n/a
12	MAZ	chr19:19515842-19516724	GM12878	blood:	n/a	chr19:19516393-19516403
13	ZBTB7A	chr19:19516615-19517724	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr19:19515949-19516729	K562	blood:	n/a	n/a
15	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
16	POLR2A	chr19:19516088-19516750	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr19:19515971-19516837	HL-60	blood:	n/a	n/a
18	POLR2A	chr19:19516014-19516808	Gliobla	brain:	n/a	n/a
19	TAF1	chr19:19516383-19516689	GM12878	blood:	n/a	n/a
20	E2F1	chr19:19515994-19516735	Hela-S3	cervix:	n/a	chr19:19516596-19516606 chr19:19516392-19516401 chr19:19516597-19516607
21	POLR2A	chr19:19515810-19518478	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr19:19515634-19518501	SK-N-SH	brain:	n/a	chr19:19517040-19517049
23	JUND	chr19:19515978-19516732	A549	lung:	n/a	chr19:19516195-19516206 chr19:19516195-19516207 chr19:19516197-19516205
24	CREB1	chr19:19515964-19516824	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:19516000-19516727	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:19516031-19516897	MCF-7	breast:	n/a	n/a
27	MXI1	chr19:19515533-19518803	IMR90	lung:	n/a	chr19:19517040-19517049
28	NRF1	chr19:19516054-19516771	GM12878	blood:	n/a	chr19:19516434-19516443 chr19:19516392-19516401 chr19:19516593-19516604 chr19:19516574-19516585
29	CREB1	chr19:19516025-19516791	H1-hESC	embryonic stem cell:	n/a	n/a
30	MYC	chr19:19516157-19516700	HepG2	liver:	n/a	chr19:19516393-19516403
31	MAX	chr19:19515703-19516686	ECC-1	luminal epithelium:	n/a	chr19:19516393-19516403
32	POLR2A	chr19:19516013-19517615	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr19:19516121-19516851	NB4	blood:	n/a	n/a
34	HDAC2	chr19:19515960-19516700	MCF-7	breast:	n/a	n/a
35	MAZ	chr19:19515942-19516714	HepG2	liver:	n/a	chr19:19516393-19516403
36	POLR2A	chr19:19515997-19516805	K562	blood:	n/a	n/a
37	CCNT2	chr19:19515966-19517483	K562	blood:	n/a	chr19:19516905-19516914 chr19:19517217-19517226 chr19:19516466-19516475 chr19:19516853-19516862 chr19:19517111-19517120 chr19:19516392-19516401 chr19:19516860-19516869
38	YY1	chr19:19516038-19516752	GM12878	blood:	n/a	chr19:19516392-19516401
39	SP1	chr19:19515772-19516708	HCT-116	colon:	n/a	chr19:19516390-19516401 chr19:19516391-19516405 chr19:19516039-19516048 chr19:19516391-19516400 chr19:19516038-19516052 chr19:19516038-19516047 chr19:19516432-19516444 chr19:19516391-19516400 chr19:19516390-19516402 chr19:19516037-19516049 chr19:19516464-19516476 chr19:19516433-19516443 chr19:19516392-19516401 chr19:19516391-19516401 chr19:19516433-19516442 chr19:19516390-19516402 chr19:19516037-19516049 chr19:19516466-19516475 chr19:19516433-19516443 chr19:19516391-19516401 chr19:19516465-19516475 chr19:19516464-19516476 chr19:19516433-19516442 chr19:19516411-19516422 chr19:19516359-19516370 chr19:19516465-19516475 chr19:19516434-19516443 chr19:19516432-19516444 chr19:19516465-19516474 chr19:19516038-19516048 chr19:19516465-19516474
40	POLR2A	chr19:19515764-19517712	K562	blood:	n/a	n/a
41	POLR2A	chr19:19516005-19517344	H1-hESC	embryonic stem cell:	n/a	n/a
42	ETS1	chr19:19515990-19516732	K562	blood:	n/a	chr19:19516392-19516403
43	NR2F2	chr19:19515704-19516688	K562	blood:	n/a	n/a
44	POLR2A	chr19:19516508-19516728	SK-N-SH	brain:	n/a	n/a
45	CREB1	chr19:19515943-19516718	GM12878	blood:	n/a	n/a
46	YY1	chr19:19516012-19517025	K562	blood:	n/a	chr19:19516392-19516401 chr19:19516860-19516871 chr19:19516850-19516864 chr19:19516853-19516862
47	POLR2A	chr19:19516497-19516693	HepG2	liver:	n/a	n/a
48	MYC	chr19:19516012-19517493	NB4	blood:	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
49	IRF1	chr19:19515608-19516705	K562	blood:	n/a	chr19:19516462-19516476 chr19:19516359-19516373 chr19:19516388-19516402
50	MAX	chr19:19515715-19516703	SK-N-SH	brain:	n/a	chr19:19516393-19516403

No.	Distal block	Cell Line	Cell type
1	chr19:19515119..19517741-chr19:19568755..19571176,2	MCF-7	breast:
2	chr19:19516568..19518207-chr19:19573514..19577628,3	MCF-7	breast:
3	chr19:19496016..19496749-chr19:19516167..19516951,2	K562	blood:
4	chr19:19028947..19031173-chr19:19514626..19517474,2	K562	blood:
5	chr19:19515140..19518800-chr19:19574675..19578008,3	K562	blood:
6	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
7	chr19:19514082..19516953-chr19:19567668..19570496,2	K562	blood:
8	chr19:19514894..19516950-chr19:19536458..19538380,2	MCF-7	breast:
9	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
10	chr19:19516170..19518046-chr20:30944497..30946734,2	K562	blood:
11	chr19:19428553..19432587-chr19:19515649..19520173,6	K562	blood:
12	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:
13	chr12:122985085..122985747-chr19:19516157..19516988,2	Hela-S3	cervix:
14	chr19:19494732..19500297-chr19:19512585..19520288,14	MCF-7	breast:
15	chr19:19454032..19456725-chr19:19515938..19518682,3	K562	blood:
16	chr19:19514840..19518062-chr19:19543803..19546421,4	K562	blood:
17	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267234	TF binding region
ENSG00000171456	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000207821	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000167491	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	chr19:19515400-19517600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:19515600-19517600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19515600-19517600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:19515600-19517800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:19515600-19517800	Active TSS	Colon Smooth Muscle	Colon
6	chr19:19515600-19517800	Active TSS	Fetal Kidney	kidney
7	chr19:19515600-19518000	Active TSS	Brain Anterior Caudate	brain
8	chr19:19515600-19518200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:19515800-19517400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:19515800-19517400	Active TSS	Brain Angular Gyrus	brain
11	chr19:19515800-19517400	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:19515800-19517600	Active TSS	Brain Germinal Matrix	brain
13	chr19:19515800-19517600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:19515800-19517600	Active TSS	Fetal Stomach	stomach
15	chr19:19515800-19518000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:19515800-19518000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:19515800-19518000	Active TSS	Aorta	Aorta
18	chr19:19515800-19518000	Active TSS	Gastric	stomach
19	chr19:19515800-19518200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr19:19515800-19518200	Active TSS	Ovary	ovary
21	chr19:19515800-19518200	Active TSS	Psoas Muscle	Psoas
22	chr19:19515800-19518800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:19516000-19517400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr19:19516000-19517400	Active TSS	Brain Hippocampus Middle	brain
25	chr19:19516000-19517400	Weak transcription	Fetal Heart	heart
26	chr19:19516000-19517600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr19:19516000-19517600	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:19516000-19517600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19516000-19517600	Active TSS	Brain Substantia Nigra	brain
30	chr19:19516000-19517600	Active TSS	Duodenum Mucosa	Duodenum
31	chr19:19516000-19517600	Active TSS	Fetal Brain Female	brain
32	chr19:19516000-19517600	Active TSS	Fetal Lung	lung
33	chr19:19516000-19517600	Active TSS	Placenta Amnion	Placenta Amnion
34	chr19:19516000-19517600	Active TSS	Rectal Smooth Muscle	rectum
35	chr19:19516000-19517600	Active TSS	HSMM	muscle
36	chr19:19516000-19517600	Active TSS	NHDF-Ad	bronchial
37	chr19:19516000-19517800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19516000-19517800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:19516000-19517800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:19516000-19517800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:19516000-19517800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:19516000-19517800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:19516000-19517800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr19:19516000-19518000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:19516000-19518000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:19516000-19518000	Active TSS	Right Atrium	heart
47	chr19:19516000-19518000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr19:19516000-19518200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:19516000-19518200	Active TSS	Small Intestine	intestine
50	chr19:19516200-19516800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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