Variant report

Variant	rs372238324
Chromosome Location	chr19:40005712-40005713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:102)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:102 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:40005620-40005770	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr19:40005693-40005796	GM12878	blood:	n/a	n/a
3	SIN3A	chr19:40005278-40006947	H1-hESC	embryonic stem cell:	n/a	chr19:40006693-40006706
4	CTCF	chr19:40005640-40005790	GM12874	blood:	n/a	n/a
5	TEAD4	chr19:40005576-40006298	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr19:40005641-40006237	H1-hESC	embryonic stem cell:	n/a	chr19:40005806-40005815
7	RAD21	chr19:40005543-40006198	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr19:40005568-40006068	K562	blood:	n/a	n/a
9	CTCF	chr19:40005708-40005806	K562	blood:	n/a	n/a
10	MYC	chr19:40005527-40006265	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr19:40003820-40007253	PANC-1	pancreas:	n/a	chr19:40006697-40006706
12	CTCF	chr19:40005620-40005770	HEK293	kidney:	n/a	n/a
13	RAD21	chr19:40005567-40005874	HepG2	liver:	n/a	n/a
14	CTCF	chr19:40005640-40005790	HMEC	breast:	n/a	n/a
15	CTCF	chr19:40005690-40005815	GM19238	blood:	n/a	n/a
16	ZBTB7A	chr19:40005674-40005900	HepG2	liver:	n/a	n/a
17	TAF1	chr19:40005681-40006736	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:40005620-40005770	Caco-2	colon:	n/a	n/a
19	CTCF	chr19:40005680-40005830	AG09319	gingival:	n/a	n/a
20	CTCF	chr19:40005640-40005790	AG09309	skin:	n/a	n/a
21	CTCF	chr19:40005680-40005830	HRE	kidney:	n/a	n/a
22	CTCF	chr19:40005660-40005810	GM12871	blood:	n/a	n/a
23	CTCF	chr19:40005576-40005838	GM12891	blood:	n/a	n/a
24	BACH1	chr19:40005623-40006251	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr19:40005353-40006395	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr19:40005680-40005830	HBMEC	blood vessel:	n/a	n/a
27	MAX	chr19:40005628-40005850	K562	blood:	n/a	n/a
28	ZNF143	chr19:40005428-40006261	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:40005660-40005810	GM06990	blood:	n/a	n/a
30	YY1	chr19:40005565-40006762	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZNF263	chr19:40005149-40005727	HEK293-T-REx	kidney:	n/a	n/a
32	MAX	chr19:40005515-40006511	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr19:40005700-40005850	HepG2	liver:	n/a	n/a
34	CTCF	chr19:40005640-40005831	GM19240	blood:	n/a	n/a
35	MAX	chr19:40005460-40006565	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr19:40005547-40005922	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr19:40005620-40005770	BE2_C	brain:	n/a	n/a
38	CTCF	chr19:40005680-40005830	GM12873	blood:	n/a	n/a
39	CREB1	chr19:40005477-40006309	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr19:40005680-40005830	HepG2	liver:	n/a	n/a
41	SP1	chr19:40005606-40006459	H1-hESC	embryonic stem cell:	n/a	chr19:40005662-40005671
42	CTCF	chr19:40005520-40005901	K562	blood:	n/a	n/a
43	RAD21	chr19:40005286-40006191	H1-hESC	embryonic stem cell:	n/a	n/a
44	SP1	chr19:40005663-40006396	A549	lung:	n/a	n/a
45	CTCF	chr19:40005600-40005750	K562	blood:	n/a	n/a
46	SIN3AK20	chr19:40002596-40007321	PANC-1	pancreas:	n/a	n/a
47	CTBP2	chr19:40005508-40006510	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr19:40005680-40005830	GM12872	blood:	n/a	n/a
49	CTCF	chr19:40005640-40005790	GM12869	blood:	n/a	n/a
50	CTCF	chr19:40005712-40005769	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40005667-40005717	AoSMC	blood vessel:	n/a
2	chr19:40005667-40005717	SKMC	muscle:	n/a
3	chr19:40005667-40005717	HCPEpiC	choroid plexus:	n/a
4	chr19:40005667-40005717	HCT-116	colon:	n/a
5	chr19:40005667-40005717	HNPCEpiC	eye:	n/a
6	chr19:40005667-40005717	Caco-2	colon:	n/a
7	chr19:40005667-40005717	SK-N-SH_RA	brain:	n/a
8	chr19:40005667-40005717	BJ	skin:	n/a
9	chr19:40005667-40005717	HRE	kidney:	n/a
10	chr19:40005667-40005717	HPAEpiC	pulmonary alveolar:	n/a
11	chr19:40005667-40005717	PANC-1	pancreas:	n/a
12	chr19:40005667-40005717	Hela-S3	cervix:	n/a
13	chr19:40005667-40005717	GM19239	blood:	n/a
14	chr19:40005667-40005717	LNCaP	prostate:	n/a
15	chr19:40005667-40005717	AG04449	skin:	fetal
16	chr19:40005667-40005717	CMK	blood:	n/a
17	chr19:40005667-40005717	MCF10A-Er-Src	breast:	n/a
18	chr19:40005667-40005717	Jurkat	blood:	n/a
19	chr19:40005667-40005717	ovcar-3	ovarian:	n/a
20	chr19:40005667-40005717	HepG2	liver:	n/a
21	chr19:40005667-40005717	IMR90	lung:	fetal
22	chr19:40005667-40005717	SK-N-MC	brain:	n/a
23	chr19:40005667-40005717	AG10803	skin:	n/a
24	chr19:40005667-40005717	HUVEC	blood vessel:	n/a
25	chr19:40005667-40005717	PFSK-1	brain:	n/a
26	chr19:40005667-40005717	HEEpiC	esophagus:	n/a
27	chr19:40005667-40005717	MCF-7	breast:	n/a
28	chr19:40005667-40005717	ECC-1	luminal epithelium:	n/a
29	chr19:40005667-40005717	HEK293	kidney:	embryo
30	chr19:40005667-40005717	SAEC	small airway:	n/a
31	chr19:40005667-40005717	RPTEC	kidney:	n/a
32	chr19:40005667-40005717	HIPEpiC	eye:	n/a
33	chr19:40005667-40005717	HAEpiC	amniotic membrane:	n/a
34	chr19:40005667-40005717	GM12892	blood:	n/a
35	chr19:40005667-40005717	HL-60	blood:	n/a
36	chr19:40005667-40005717	GM12878	blood:	n/a
37	chr19:40005667-40005717	HCM	heart:	n/a
38	chr19:40005667-40005717	AG04450	lung:	fetal
39	chr19:40005667-40005717	NHDF-neo	bronchial:	n/a
40	chr19:40005667-40005717	HRCEpiC	kidney:	n/a
41	chr19:40005667-40005717	K562	blood:	n/a
42	chr19:40005667-40005717	NH-A	brain:	n/a
43	chr19:40005667-40005717	PrEC	prostate:	n/a
44	chr19:40005667-40005717	ProgFib	skin:	n/a
45	chr19:40005667-40005717	GM12891	blood:	n/a
46	chr19:40005667-40005717	T-47D	breast:	n/a
47	chr19:40005667-40005717	SK-N-SH	brain:	n/a
48	chr19:40005667-40005717	HCF	heart:	n/a
49	chr19:40005667-40005717	A549	lung:	n/a
50	chr19:40005667-40005717	NHBE	bronchial:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39987217..39989716-chr19:40005337..40006880,2	MCF-7	breast:
2	chr19:39935872..39937858-chr19:40003816..40005942,2	MCF-7	breast:
3	chr19:39926370..39927938-chr19:40004340..40006529,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000186838	TF binding region
ENSG00000186838	CpG island
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000090932	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv3374976	chr19:39998161-40023263	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv522811	chr19:40004640-40008220	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40005200-40005800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:40005200-40006000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
3	chr19:40005200-40006600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:40005200-40007200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:40005200-40007400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:40005200-40007800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:40005400-40005800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40005400-40005800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:40005400-40005800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:40005400-40005800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr19:40005400-40005800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr19:40005400-40005800	Bivalent Enhancer	Esophagus	oesophagus
13	chr19:40005400-40005800	Bivalent Enhancer	Placenta	Placenta
14	chr19:40005400-40005800	Bivalent/Poised TSS	NHEK	skin
15	chr19:40005400-40006000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:40005400-40006000	Bivalent Enhancer	Primary B cells from cord blood	blood
17	chr19:40005400-40006000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:40005400-40006000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:40005400-40006000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:40005400-40006000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
21	chr19:40005400-40006000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:40005400-40006000	Bivalent Enhancer	Fetal Thymus	thymus
23	chr19:40005400-40006000	Bivalent Enhancer	Left Ventricle	heart
24	chr19:40005400-40006000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr19:40005400-40006200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
26	chr19:40005400-40006200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:40005400-40006200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:40005400-40006200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
29	chr19:40005400-40006400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
30	chr19:40005400-40006600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:40005400-40006600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:40005400-40006600	Bivalent Enhancer	Fetal Lung	lung
33	chr19:40005400-40006600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
34	chr19:40005400-40006600	Bivalent Enhancer	Stomach Mucosa	stomach
35	chr19:40005400-40006800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
36	chr19:40005400-40006800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr19:40005400-40006800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:40005400-40006800	Flanking Active TSS	Right Ventricle	heart
39	chr19:40005400-40006800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr19:40005400-40007000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr19:40005400-40007000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr19:40005400-40007200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:40005400-40007200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:40005400-40007200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:40005400-40007200	Active TSS	Fetal Kidney	kidney
46	chr19:40005600-40005800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:40005600-40005800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr19:40005600-40005800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr19:40005600-40005800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:40005600-40005800	Flanking Active TSS	Brain Angular Gyrus	brain

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