Variant report

Variant	rs7254360
Chromosome Location	chr19:36979961-36979962
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	MYC	chr19:36979863-36980167	GM12878	blood:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980138-36980153 chr19:36980142-36980152
2	MYC	chr19:36979780-36980760	HepG2	liver:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
3	SIN3AK20	chr19:36979674-36980602	K562	blood:	n/a	n/a
4	STAT5A	chr19:36979934-36980269	GM12878	blood:	n/a	n/a
5	BHLHE40	chr19:36979860-36980623	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:36979648-36981467	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:36979664-36981112	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr19:36979662-36981378	GM12892	blood:	n/a	n/a
9	SIN3A	chr19:36979758-36981099	H1-hESC	embryonic stem cell:	n/a	chr19:36980119-36980130
10	MAX	chr19:36979766-36980843	H1-hESC	embryonic stem cell:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
11	TAF1	chr19:36979637-36981061	H1-neurons	neurons:	n/a	n/a
12	CHD2	chr19:36979768-36981002	HepG2	liver:	n/a	n/a
13	MYC	chr19:36979823-36980417	Hela-S3	cervix:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
14	POLR2A	chr19:36979816-36980965	K562	blood:	n/a	n/a
15	MAX	chr19:36979707-36981049	H1-hESC	embryonic stem cell:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
16	MTA3	chr19:36979706-36981445	GM12878	blood:	n/a	n/a
17	CTCF	chr19:36979787-36980029	ProgFib	skin:	n/a	n/a
18	ZBTB33	chr19:36979660-36981331	A549	lung:	n/a	chr19:36980475-36980490
19	BCL3	chr19:36979628-36981249	A549	lung:	n/a	chr19:36981235-36981244 chr19:36980891-36980904
20	TFAP2A	chr19:36979891-36981041	Hela-S3	cervix:	n/a	chr19:36980438-36980453
21	MAX	chr19:36979690-36981211	NB4	blood:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
22	POLR2A	chr19:36979663-36981312	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr19:36979734-36981148	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F4	chr19:36979487-36980750	MCF10A-Er-Src	breast:	n/a	n/a
25	REST	chr19:36979741-36981152	HL-60	blood:	n/a	chr19:36980350-36980363
26	E2F6	chr19:36979923-36980652	H1-hESC	embryonic stem cell:	n/a	n/a
27	MYC	chr19:36979715-36980885	K562	blood:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
28	MXI1	chr19:36978905-36981196	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr19:36979699-36980912	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr19:36979960-36980110	GM12866	blood:	n/a	n/a
31	HCFC1	chr19:36979141-36981381	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:36979736-36981466	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:36979728-36981268	GM12878	blood:	n/a	n/a
34	TAF1	chr19:36979960-36981083	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr19:36979845-36979963	H1-hESC	embryonic stem cell:	n/a	n/a
36	CHD2	chr19:36979798-36981053	K562	blood:	n/a	n/a
37	POLR2A	chr19:36979961-36981188	MCF10A-Er-Src	breast:	n/a	n/a
38	USF1	chr19:36979959-36980992	A549	lung:	n/a	n/a
39	CHD2	chr19:36979733-36981206	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:36979889-36981256	GM18951	blood:	n/a	n/a
41	ELF1	chr19:36979713-36981312	GM12878	blood:	n/a	chr19:36980344-36980356
42	MAX	chr19:36979685-36981153	H1-hESC	embryonic stem cell:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
43	GATA1	chr19:36979682-36981264	PBDE	blood:	n/a	chr19:36980877-36980886 chr19:36981083-36981092 chr19:36980877-36980887 chr19:36980877-36980886 chr19:36981218-36981228 chr19:36980868-36980885
44	MYC	chr19:36979820-36980870	H1-hESC	embryonic stem cell:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
45	MAX	chr19:36979718-36981143	HepG2	liver:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
46	SIN3AK20	chr19:36979946-36980620	HepG2	liver:	n/a	n/a
47	MYC	chr19:36979762-36980642	MCF-7	breast:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
48	MAX	chr19:36979680-36981171	HepG2	liver:	n/a	chr19:36980143-36980150 chr19:36980140-36980155 chr19:36980143-36980152 chr19:36980142-36980151 chr19:36980350-36980360 chr19:36980138-36980153 chr19:36980142-36980152
49	CREB1	chr19:36979724-36981245	HepG2	liver:	n/a	n/a
50	POLR2A	chr19:36979808-36981069	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36969427..36971707-chr19:36977964..36979970,2	MCF-7	breast:
2	chr19:36704032..36706423-chr19:36978429..36980490,2	MCF-7	breast:
3	chr19:36979193..36981748-chr19:37061672..37065426,4	K562	blood:
4	chr19:36979208..36981780-chr19:37261367..37264210,2	K562	blood:
5	chr19:36979933..36980756-chr6:30711805..30712354,2	HCT-116	colon:
6	chr19:36704170..36706461-chr19:36978975..36980989,3	K562	blood:
7	chr19:36706883..36709067-chr19:36978381..36980309,2	K562	blood:
8	chr19:36979323..36981752-chr19:37018816..37021173,2	MCF-7	breast:
9	chr19:36979379..36982047-chr19:37063909..37066157,2	K562	blood:
10	chr19:36867662..36870599-chr19:36976598..36980024,4	K562	blood:
11	chr19:36979900..36980804-chr9:127624247..127624899,2	Hela-S3	cervix:
12	chr19:36979124..36982554-chr19:37017679..37020247,4	MCF-7	breast:
13	chr19:36978237..36981071-chr19:36988174..36990152,2	K562	blood:
14	chr19:36978148..36981795-chr19:37018105..37021194,8	K562	blood:
15	chr19:36978821..36980790-chr19:37017858..37020685,3	K562	blood:
16	chr19:36978237..36981428-chr19:36988174..36990245,3	K562	blood:

Variant related genes	Relation type
ENSG00000267309	TF binding region
ENSG00000136942	Chromatin interaction
ENSG00000267091	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000142065	Chromatin interaction
ENSG00000196357	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000266973	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000136950	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs35217571	0.82[AFR][1000 genomes]
rs58453309	1.00[AFR][1000 genomes]
rs59860141	0.90[AFR][1000 genomes]
rs61616528	0.95[AFR][1000 genomes]
rs7255284	0.90[AFR][1000 genomes]
rs7258723	0.82[AFR][1000 genomes]
rs8101921	1.00[AFR][1000 genomes]
rs8107110	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs8113012	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs8113549	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 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	chr19:36978400-36981400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:36978800-36981000	Active TSS	K562	blood
3	chr19:36979000-36980000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:36979000-36980000	Flanking Active TSS	Dnd41	blood
5	chr19:36979000-36981000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:36979000-36981400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:36979000-36981400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:36979000-36981400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:36979000-36981400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr19:36979200-36980000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr19:36979200-36980000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:36979200-36980000	Flanking Active TSS	NHLF	lung
13	chr19:36979200-36980200	Flanking Active TSS	Liver	Liver
14	chr19:36979200-36980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:36979200-36981000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:36979200-36981000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:36979200-36981200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr19:36979200-36981400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:36979200-36981400	Active TSS	Muscle Satellite Cultured Cells	--
20	chr19:36979200-36981400	Active TSS	Fetal Brain Female	brain
21	chr19:36979200-36981400	Active TSS	HSMM	muscle
22	chr19:36979400-36980000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr19:36979400-36980000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:36979400-36980000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr19:36979400-36980000	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr19:36979400-36980000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr19:36979400-36980000	Flanking Active TSS	Fetal Brain Male	brain
28	chr19:36979400-36980000	Flanking Active TSS	Osteobl	bone
29	chr19:36979400-36980200	Flanking Active TSS	NHEK	skin
30	chr19:36979400-36980400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr19:36979400-36980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:36979400-36981000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:36979400-36981000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr19:36979400-36981000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:36979400-36981200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:36979400-36981200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:36979400-36981400	Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:36979400-36981400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:36979400-36981400	Active TSS	Fetal Intestine Large	intestine
40	chr19:36979400-36981400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr19:36979400-36981400	Active TSS	Right Ventricle	heart
42	chr19:36979400-36981400	Active TSS	Hela-S3	cervix
43	chr19:36979400-36981400	Active TSS	NHDF-Ad	bronchial
44	chr19:36979400-36981600	Active TSS	GM12878-XiMat	blood
45	chr19:36979600-36980000	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr19:36979600-36980000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr19:36979600-36980000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:36979600-36980000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr19:36979600-36980000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:36979600-36980000	Flanking Active TSS	Brain Angular Gyrus	brain

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