Variant report

Variant	rs564996154
Chromosome Location	chr19:42905590-42905591
allele	C/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	RAD21	chr19:42905466-42905716	HepG2	liver:	n/a	chr19:42905470-42905484 chr19:42905616-42905628 chr19:42905618-42905628 chr19:42905617-42905630 chr19:42905614-42905633
2	GABPA	chr19:42905351-42905844	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr19:42905495-42905796	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr19:42905560-42905710	HCFaa	heart:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
5	RAD21	chr19:42905410-42905842	ECC-1	luminal epithelium:	n/a	chr19:42905470-42905484 chr19:42905616-42905628 chr19:42905618-42905628 chr19:42905617-42905630 chr19:42905614-42905633
6	CREB1	chr19:42905388-42906508	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr19:42905540-42905690	HMF	breast:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
8	CTCF	chr19:42905538-42905767	GM10248	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
9	CTCF	chr19:42905540-42905690	HVMF	connective:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
10	CTCF	chr19:42905495-42905774	MCF-7	breast:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
11	CTCF	chr19:42905427-42906235	GM12878	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
12	RAD21	chr19:42905464-42905784	Hela-S3	cervix:	n/a	chr19:42905470-42905484 chr19:42905616-42905628 chr19:42905618-42905628 chr19:42905617-42905630 chr19:42905614-42905633
13	CTCF	chr19:42905560-42905710	HRE	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
14	BCL3	chr19:42904890-42906637	A549	lung:	n/a	n/a
15	CTCF	chr19:42905540-42905690	HEK293	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
16	CTCF	chr19:42905540-42905690	GM12866	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
17	CTCF	chr19:42905560-42905710	HUVEC	blood vessel:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
18	PBX3	chr19:42905074-42907464	A549	lung:	n/a	n/a
19	CTCF	chr19:42905580-42905730	MCF-7	breast:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
20	CTCF	chr19:42905500-42905650	HEK293	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
21	YY1	chr19:42905470-42905794	A549	lung:	n/a	n/a
22	CTCF	chr19:42905444-42905871	GM19238	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
23	CTCF	chr19:42905540-42905690	GM12864	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
24	CTCF	chr19:42905566-42905731	GM20000	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
25	WRNIP1	chr19:42905573-42905773	GM12878	blood:	n/a	n/a
26	CTCF	chr19:42905505-42905776	HUVEC	blood vessel:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
27	CTCF	chr19:42905540-42905690	HRE	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
28	POLR2A	chr19:42905489-42906437	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr19:42905580-42905730	AG04449	skin:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
30	CTCF	chr19:42905200-42907189	SK-N-SH	brain:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
31	CTCF	chr19:42905500-42905650	HUVEC	blood vessel:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
32	CTCF	chr19:42905520-42905670	GM12873	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
33	CTCF	chr19:42905462-42905817	A549	lung:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
34	TAF7	chr19:42905383-42905804	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr19:42905520-42905764	MCF-7	breast:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
36	ARID3A	chr19:42905478-42905731	K562	blood:	n/a	n/a
37	CTCF	chr19:42905297-42905780	A549	lung:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
38	TBL1XR1	chr19:42905488-42905647	K562	blood:	n/a	n/a
39	CTCF	chr19:42905560-42905710	WERI-Rb-1	eye:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
40	MAX	chr19:42905552-42905728	GM12878	blood:	n/a	n/a
41	CTCF	chr19:42905520-42905670	AG09319	gingival:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
42	CTCF	chr19:42905560-42905710	SK-N-SH_RA	brain:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
43	CHD2	chr19:42905415-42905719	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr19:42905540-42905690	AG04449	skin:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
45	CTCF	chr19:42905520-42905670	K562	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
46	CTCF	chr19:42905507-42905797	Kidney_OC	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
47	CTCF	chr19:42905560-42905710	HEEpiC	esophagus:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
48	SP1	chr19:42905393-42905762	GM12878	blood:	n/a	n/a
49	CTCF	chr19:42905560-42905710	RPTEC	kidney:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
50	CTCF	chr19:42905475-42905799	GM12878	blood:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634

No.	Distal block	Cell Line	Cell type
1	chr19:42900819..42903655-chr19:42904775..42907143,2	MCF-7	breast:
2	chr19:42904315..42908218-chr19:42909528..42916555,10	K562	blood:
3	chr19:42829022..42830328-chr19:42905348..42906313,3	MCF-7	breast:
4	chr19:42900633..42903687-chr19:42904617..42908034,6	MCF-7	breast:
5	chr19:42636919..42637858-chr19:42905037..42905701,9	K562	blood:
6	chr19:42904602..42907517-chr19:42908247..42910710,2	MCF-7	breast:
7	chr19:42583843..42585623-chr19:42905148..42907036,2	MCF-7	breast:
8	chr19:42786293..42789026-chr19:42903312..42906811,3	MCF-7	breast:
9	chr19:42771317..42774035-chr19:42904213..42905727,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000079435	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000268525	Chromatin interaction
ENSG00000105429	Chromatin interaction
ENSG00000213904	Chromatin interaction
ENSG00000266226	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv911789	chr19:42901430-42906725	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv911790	chr19:42901430-42908074	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv911791	chr19:42901430-42909478	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv911792	chr19:42901430-42929254	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv911793	chr19:42901430-42929502	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv911794	chr19:42901430-42930652	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv911795	chr19:42901430-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv579630	chr19:42904238-42906383	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
16	nsv911796	chr19:42904388-42906914	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
17	nsv579631	chr19:42904653-42906741	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
18	nsv911797	chr19:42904653-42906914	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
19	nsv579632	chr19:42904653-42912403	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
20	nsv911798	chr19:42904653-42930652	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42902200-42905600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:42902200-42905600	Weak transcription	Small Intestine	intestine
3	chr19:42902400-42905600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:42903200-42905600	Weak transcription	Gastric	stomach
5	chr19:42903200-42905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:42904200-42905600	Enhancers	Pancreas	Pancrea
7	chr19:42904400-42905600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:42904600-42905600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:42904800-42905600	Enhancers	Primary B cells from cord blood	blood
10	chr19:42904800-42905800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:42904800-42906800	Enhancers	Fetal Heart	heart
12	chr19:42905000-42905600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:42905000-42905600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr19:42905000-42906600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:42905000-42907000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr19:42905000-42907000	Enhancers	Spleen	Spleen
17	chr19:42905200-42905600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:42905200-42905600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:42905200-42905600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:42905200-42905600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:42905200-42905600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr19:42905200-42905600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr19:42905200-42905600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr19:42905200-42905600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:42905200-42905600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr19:42905200-42905600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr19:42905200-42905600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:42905200-42905600	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr19:42905200-42905800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:42905200-42905800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:42905200-42905800	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr19:42905200-42905800	Flanking Active TSS	Esophagus	oesophagus
33	chr19:42905200-42906000	Enhancers	Adipose Nuclei	Adipose
34	chr19:42905200-42906200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:42905200-42906200	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr19:42905200-42906400	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr19:42905200-42906400	Enhancers	Stomach Mucosa	stomach
38	chr19:42905200-42906600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:42905200-42906600	Active TSS	Fetal Kidney	kidney
40	chr19:42905200-42906800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:42905200-42906800	Active TSS	A549	lung
42	chr19:42905200-42907000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:42905400-42905600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:42905400-42905600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:42905400-42905600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:42905400-42905600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:42905400-42905600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:42905400-42905600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr19:42905400-42905600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr19:42905400-42905600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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