Variant report

Variant	rs73934402
Chromosome Location	chr19:56159470-56159471
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	SIN3A	chr19:56159031-56160360	GM12878	blood:	n/a	chr19:56159842-56159853
2	POLR2A	chr19:56158426-56160162	K562	blood:	n/a	n/a
3	BACH1	chr19:56159157-56160068	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr19:56159313-56159585	A549	lung:	n/a	chr19:56159516-56159526
5	FAM48A	chr19:56159109-56159757	GM12878	blood:	n/a	n/a
6	TCF12	chr19:56158737-56160156	A549	lung:	n/a	chr19:56159516-56159526
7	POLR2A	chr19:56158684-56159850	HEK293	kidney:	n/a	n/a
8	POLR2A	chr19:56159191-56160044	A549	lung:	n/a	n/a
9	SP1	chr19:56159014-56160080	A549	lung:	n/a	chr19:56159336-56159350 chr19:56159890-56159902 chr19:56159844-56159858 chr19:56159891-56159901 chr19:56159896-56159906 chr19:56159890-56159902 chr19:56159891-56159900 chr19:56159340-56159349 chr19:56159339-56159350
10	TBL1XR1	chr19:56159201-56159841	K562	blood:	n/a	n/a
11	E2F6	chr19:56159450-56159646	K562	blood:	n/a	chr19:56159587-56159597 chr19:56159516-56159526 chr19:56159586-56159596
12	SIN3AK20	chr19:56159012-56159484	A549	lung:	n/a	n/a
13	CREB1	chr19:56159071-56159993	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:56159258-56159715	K562	blood:	n/a	n/a
15	HCFC1	chr19:56159190-56160037	K562	blood:	n/a	n/a
16	ZNF143	chr19:56159161-56159671	K562	blood:	n/a	chr19:56159587-56159597 chr19:56159586-56159596
17	CREB1	chr19:56159067-56159667	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr19:56159189-56159505	SK-N-SH	brain:	n/a	n/a
19	MAX	chr19:56159137-56160203	A549	lung:	n/a	chr19:56159340-56159350 chr19:56159809-56159818 chr19:56159876-56159885 chr19:56159689-56159699 chr19:56159764-56159774
20	YY1	chr19:56159078-56160052	HepG2	liver:	n/a	chr19:56159601-56159610 chr19:56159925-56159939 chr19:56159891-56159902 chr19:56159512-56159523 chr19:56159604-56159613
21	CEBPD	chr19:56159225-56159938	HepG2	liver:	n/a	n/a
22	ZNF143	chr19:56159116-56159981	GM12878	blood:	n/a	chr19:56159689-56159699 chr19:56159689-56159707 chr19:56159587-56159597 chr19:56159586-56159596
23	POLR2A	chr19:56159129-56160028	HUVEC	blood vessel:	n/a	n/a
24	HDAC2	chr19:56159355-56159961	K562	blood:	n/a	chr19:56159876-56159885 chr19:56159496-56159515
25	CEBPB	chr19:56159183-56159485	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:56159236-56160304	MCF-7	breast:	n/a	n/a
27	CHD2	chr19:56159227-56159558	HepG2	liver:	n/a	n/a
28	EBF1	chr19:56158767-56159582	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:56159230-56159538	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr19:56159078-56159744	SK-N-SH_RA	brain:	n/a	chr19:56159601-56159610 chr19:56159512-56159523 chr19:56159604-56159613
31	POLR2A	chr19:56159304-56159547	HepG2	liver:	n/a	n/a
32	NFIC	chr19:56158652-56159538	ECC-1	luminal epithelium:	n/a	n/a
33	ZMIZ1	chr19:56159122-56159598	K562	blood:	n/a	n/a
34	RCOR1	chr19:56158679-56160151	K562	blood:	n/a	n/a
35	EGR1	chr19:56159074-56159607	H1-hESC	embryonic stem cell:	n/a	chr19:56159339-56159349 chr19:56159537-56159552
36	SIN3AK20	chr19:56159317-56159814	SK-N-SH	brain:	n/a	n/a
37	NR2F2	chr19:56159398-56159735	K562	blood:	n/a	n/a
38	YY1	chr19:56159155-56159650	H1-hESC	embryonic stem cell:	n/a	chr19:56159601-56159610 chr19:56159512-56159523 chr19:56159604-56159613
39	RUNX3	chr19:56158619-56160103	GM12878	blood:	n/a	n/a
40	TBL1XR1	chr19:56159118-56159922	K562	blood:	n/a	n/a
41	YY1	chr19:56159154-56159800	ECC-1	luminal epithelium:	n/a	chr19:56159601-56159610 chr19:56159512-56159523 chr19:56159604-56159613
42	STAT5A	chr19:56159136-56159524	GM12878	blood:	n/a	chr19:56159342-56159354 chr19:56159337-56159349
43	SP1	chr19:56159082-56159995	GM12878	blood:	n/a	chr19:56159336-56159350 chr19:56159890-56159902 chr19:56159844-56159858 chr19:56159891-56159901 chr19:56159896-56159906 chr19:56159890-56159902 chr19:56159891-56159900 chr19:56159340-56159349 chr19:56159339-56159350
44	POLR2A	chr19:56159066-56160080	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:56159063-56160005	H1-neurons	neurons:	n/a	n/a
46	EGR1	chr19:56159174-56160094	K562	blood:	n/a	chr19:56159886-56159899 chr19:56159875-56159885 chr19:56159882-56159904 chr19:56159339-56159349 chr19:56159874-56159887 chr19:56159888-56159898 chr19:56159886-56159899 chr19:56159846-56159859 chr19:56159873-56159887 chr19:56159875-56159886 chr19:56159875-56159884 chr19:56159836-56159845 chr19:56159875-56159886 chr19:56159885-56159900 chr19:56159874-56159887 chr19:56159874-56159887 chr19:56159875-56159885 chr19:56159874-56159887 chr19:56159537-56159552 chr19:56159677-56159687 chr19:56159886-56159900
47	POLR2A	chr19:56158624-56160441	GM12878	blood:	n/a	n/a
48	CREB1	chr19:56158826-56160026	A549	lung:	n/a	n/a
49	RELA	chr19:56158525-56160062	GM12891	blood:	n/a	n/a
50	MYC	chr19:56159352-56159552	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56158129..56161096-chr19:56185326..56187791,3	MCF-7	breast:

Variant related genes	Relation type
CCDC106	TF binding region
ENSG00000267523	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs56115240	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56250101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56331023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61736526	1.00[AMR][1000 genomes]
rs73933303	1.00[AMR][1000 genomes]
rs73933306	1.00[AMR][1000 genomes]
rs73933307	1.00[AMR][1000 genomes]
rs73933308	1.00[AMR][1000 genomes]
rs73934393	0.81[AFR][1000 genomes]
rs73934395	0.81[AFR][1000 genomes]
rs73934401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936310	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936311	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936316	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 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	chr19:56158200-56160800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr19:56158200-56161800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:56158400-56159800	Enhancers	Fetal Brain Male	brain
4	chr19:56158400-56160600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:56158400-56161000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:56158400-56161200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr19:56158600-56159800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:56158600-56160000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:56158600-56160800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:56158600-56160800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr19:56158800-56159800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:56158800-56160000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:56158800-56160200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr19:56158800-56160400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr19:56158800-56160400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr19:56158800-56160400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:56158800-56160400	Active TSS	HSMMtube	muscle
18	chr19:56159000-56159600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr19:56159000-56159800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:56159000-56159800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr19:56159000-56159800	Active TSS	Gastric	stomach
22	chr19:56159000-56160000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:56159000-56160000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr19:56159000-56160200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:56159000-56160200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56159000-56160200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:56159000-56160200	Active TSS	Brain Anterior Caudate	brain
28	chr19:56159000-56160200	Active TSS	Ovary	ovary
29	chr19:56159000-56160200	Active TSS	Psoas Muscle	Psoas
30	chr19:56159000-56160400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:56159000-56160400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:56159000-56160400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr19:56159000-56160400	Flanking Active TSS	HMEC	breast
34	chr19:56159000-56160600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:56159000-56160600	Flanking Active TSS	Placenta	Placenta
36	chr19:56159000-56160800	Active TSS	Fetal Kidney	kidney
37	chr19:56159000-56161000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:56159000-56161000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr19:56159200-56159600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:56159200-56159600	Active TSS	Primary hematopoietic stem cells	blood
41	chr19:56159200-56159600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:56159200-56159800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:56159200-56159800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:56159200-56159800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:56159200-56159800	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr19:56159200-56160000	Active TSS	H1 Cell Line	embryonic stem cell
47	chr19:56159200-56160000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:56159200-56160000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:56159200-56160000	Active TSS	Primary B cells from peripheral blood	blood
50	chr19:56159200-56160000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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