Variant report

Variant	rs117002420
Chromosome Location	chr19:42905253-42905254
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	BCL3	chr19:42904890-42906637	A549	lung:	n/a	n/a
2	PBX3	chr19:42905074-42907464	A549	lung:	n/a	n/a
3	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
4	CTCF	chr19:42905200-42905350	GM12868	blood:	n/a	n/a
5	CTCF	chr19:42905120-42905270	GM12872	blood:	n/a	n/a
6	CTCF	chr19:42905142-42905841	HCT-116	colon:	n/a	chr19:42905618-42905631 chr19:42905611-42905632 chr19:42905622-42905631 chr19:42905619-42905629 chr19:42905616-42905634
7	RAD21	chr19:42905208-42905959	A549	lung:	n/a	chr19:42905470-42905484 chr19:42905616-42905628 chr19:42905618-42905628 chr19:42905617-42905630 chr19:42905614-42905633
8	JUND	chr19:42905251-42906393	A549	lung:	n/a	n/a
9	POLR2A	chr19:42905147-42906543	PFSK-1	brain:	n/a	n/a
10	TCF12	chr19:42905196-42906553	A549	lung:	n/a	n/a
11	RAD21	chr19:42905249-42905849	HCT-116	colon:	n/a	chr19:42905470-42905484 chr19:42905616-42905628 chr19:42905618-42905628 chr19:42905617-42905630 chr19:42905614-42905633
12	MTA3	chr19:42904780-42905810	GM12878	blood:	n/a	n/a
13	SP1	chr19:42905170-42906550	A549	lung:	n/a	n/a
14	POLR2A	chr19:42904761-42907160	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:42905149-42906513	SK-N-SH	brain:	n/a	n/a
16	SP1	chr19:42905195-42906463	A549	lung:	n/a	n/a
17	MXI1	chr19:42905113-42907416	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr19:42905156-42907072	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr19:42905140-42905290	WI-38	lung:	n/a	n/a
20	CTCF	chr19:42904097-42906984	A549	lung:	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	chr19:42895668..42898012-chr19:42901990..42905454,3	K562	blood:
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	chr19:42903018..42905424-chr19:42908896..42911686,2	MCF-7	breast:
9	chr19:42786293..42789026-chr19:42903312..42906811,3	MCF-7	breast:
10	chr19:42771317..42774035-chr19:42904213..42905727,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000079432	Chromatin interaction
ENSG00000268525	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000213904	Chromatin interaction
ENSG00000079435	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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42901800-42905400	Weak transcription	Aorta	Aorta
2	chr19:42902200-42905400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:42902200-42905400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:42902200-42905400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:42902200-42905400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:42902200-42905400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:42902200-42905400	Weak transcription	Brain Substantia Nigra	brain
8	chr19:42902200-42905400	Weak transcription	Left Ventricle	heart
9	chr19:42902200-42905400	Weak transcription	Lung	lung
10	chr19:42902200-42905400	Weak transcription	Psoas Muscle	Psoas
11	chr19:42902200-42905400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:42902200-42905400	Weak transcription	Right Atrium	heart
13	chr19:42902200-42905400	Weak transcription	HSMM	muscle
14	chr19:42902200-42905400	Weak transcription	HSMMtube	muscle
15	chr19:42902200-42905600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:42902200-42905600	Weak transcription	Small Intestine	intestine
17	chr19:42902400-42905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:42902400-42905400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr19:42902400-42905400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:42902400-42905400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:42902400-42905400	Weak transcription	Brain Angular Gyrus	brain
22	chr19:42902400-42905400	Weak transcription	Colonic Mucosa	Colon
23	chr19:42902400-42905400	Weak transcription	Ovary	ovary
24	chr19:42902400-42905400	Weak transcription	HMEC	breast
25	chr19:42902400-42905400	Weak transcription	HUVEC	blood vessel
26	chr19:42902400-42905400	Weak transcription	NH-A	brain
27	chr19:42902400-42905400	Weak transcription	NHDF-Ad	bronchial
28	chr19:42902400-42905400	Weak transcription	NHLF	lung
29	chr19:42902400-42905400	Weak transcription	Osteobl	bone
30	chr19:42902400-42905600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:42902600-42905400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:42902600-42905400	Weak transcription	GM12878-XiMat	blood
33	chr19:42903200-42905400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:42903200-42905400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:42903200-42905600	Weak transcription	Gastric	stomach
36	chr19:42903200-42905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:42903600-42905400	Weak transcription	Right Ventricle	heart
38	chr19:42904200-42905400	Enhancers	Fetal Muscle Trunk	muscle
39	chr19:42904200-42905400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr19:42904200-42905600	Enhancers	Pancreas	Pancrea
41	chr19:42904400-42905400	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:42904400-42905400	Enhancers	Brain Cingulate Gyrus	brain
43	chr19:42904400-42905400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr19:42904400-42905600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:42904600-42905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:42904600-42905600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:42904800-42905400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr19:42904800-42905400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr19:42904800-42905600	Enhancers	Primary B cells from cord blood	blood
50	chr19:42904800-42905800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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