Variant report

Variant	rs10410833
Chromosome Location	chr19:45668327-45668328
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45667571-45668389	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:45667434-45668355	GM12878	blood:	n/a	n/a
3	ELF1	chr19:45667067-45668678	GM12878	blood:	n/a	n/a
4	YY1	chr19:45667964-45668359	K562	blood:	n/a	chr19:45668014-45668025
5	CTCF	chr19:45668260-45668410	HCT-116	colon:	n/a	chr19:45668365-45668378
6	PML	chr19:45667398-45668470	GM12878	blood:	n/a	n/a
7	SP1	chr19:45667864-45668337	A549	lung:	n/a	n/a
8	ZNF263	chr19:45667804-45668450	HEK293-T-REx	kidney:	n/a	chr19:45668275-45668284
9	CREB1	chr19:45667817-45668353	A549	lung:	n/a	n/a
10	POLR2A	chr19:45668160-45668416	ProgFib	skin:	n/a	n/a
11	POLR2A	chr19:45667561-45668407	A549	lung:	n/a	n/a
12	NFATC1	chr19:45667756-45668331	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:45667895-45668790	K562	blood:	n/a	n/a
14	MTA3	chr19:45667147-45668640	GM12878	blood:	n/a	n/a
15	EBF1	chr19:45667426-45668392	GM12878	blood:	n/a	n/a
16	TCF12	chr19:45667633-45668419	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr19:45668031-45668328	GM19239	blood:	n/a	n/a
18	CTCF	chr19:45667922-45668414	MCF-7	breast:	n/a	chr19:45667983-45667996 chr19:45668365-45668378
19	MAX	chr19:45667912-45668400	MCF-7	breast:	n/a	n/a
20	CTCF	chr19:45667915-45668368	K562	blood:	n/a	chr19:45667983-45667996
21	CTCF	chr19:45668180-45668330	GM12870	blood:	n/a	n/a
22	BCL3	chr19:45667219-45668376	A549	lung:	n/a	chr19:45667604-45667613 chr19:45668040-45668049
23	POLR2A	chr19:45667672-45668520	HL-60	blood:	n/a	n/a
24	POLR2A	chr19:45667742-45668342	ECC-1	luminal epithelium:	n/a	n/a
25	GABPA	chr19:45667847-45668409	MCF-7	breast:	n/a	n/a
26	POLR2A	chr19:45667616-45668365	GM12892	blood:	n/a	n/a
27	NR3C1	chr19:45667950-45668378	A549	lung:	n/a	n/a
28	ELF1	chr19:45667854-45668447	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45646729..45650244-chr19:45666195..45669472,3	MCF-7	breast:
2	chr19:45664293..45670548-chr19:45677917..45684715,10	MCF-7	breast:
3	chr19:45663965..45672033-chr19:45672145..45675901,9	K562	blood:
4	chr19:45579089..45581981-chr19:45667540..45670366,2	K562	blood:
5	chr19:45667124..45670268-chr19:45680467..45683235,3	K562	blood:
6	chr19:45667869..45670716-chr19:45675537..45677306,2	MCF-7	breast:
7	chr19:45664074..45668689-chr19:45680998..45684242,7	MCF-7	breast:
8	chr19:45558584..45560889-chr19:45665988..45668898,2	K562	blood:
9	chr19:45665641..45668911-chr19:45670300..45671967,3	K562	blood:
10	chr19:45665456..45669944-chr19:45672662..45676859,4	MCF-7	breast:

No data

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000267545	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000189114	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10417602	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28367893	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247764	0.98[ASN][1000 genomes]

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	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45660200-45674000	Weak transcription	A549	lung
2	chr19:45662800-45669000	Enhancers	Esophagus	oesophagus
3	chr19:45664000-45670200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:45664200-45668400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:45665400-45669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:45665400-45670000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:45665400-45670200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:45665400-45680400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:45665400-45680600	Weak transcription	Fetal Lung	lung
10	chr19:45665600-45680400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:45665800-45674600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:45665800-45680200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:45665800-45680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:45666000-45669200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr19:45666000-45669200	Enhancers	HMEC	breast
16	chr19:45666000-45669800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:45666200-45668800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr19:45666400-45668600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:45666400-45670400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:45666600-45668400	Enhancers	NHEK	skin
21	chr19:45666600-45669000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:45666600-45671000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:45666800-45668800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:45667000-45668600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr19:45667000-45669000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:45667000-45669000	Enhancers	Right Ventricle	heart
27	chr19:45667000-45669200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:45667000-45669200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:45667000-45670400	Enhancers	Fetal Thymus	thymus
30	chr19:45667000-45670600	Enhancers	Placenta	Placenta
31	chr19:45667200-45668400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr19:45667200-45668400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr19:45667200-45668400	Enhancers	Stomach Mucosa	stomach
34	chr19:45667200-45668600	Enhancers	Primary T cells from cord blood	blood
35	chr19:45667200-45668600	Enhancers	Duodenum Mucosa	Duodenum
36	chr19:45667200-45668800	Enhancers	Primary hematopoietic stem cells	blood
37	chr19:45667200-45668800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:45667200-45668800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:45667200-45669200	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:45667400-45668400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:45667400-45668400	Enhancers	Fetal Intestine Large	intestine
42	chr19:45667400-45668400	Enhancers	Fetal Intestine Small	intestine
43	chr19:45667400-45668400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr19:45667400-45668400	Enhancers	HSMM	muscle
45	chr19:45667400-45668600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:45667400-45668600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr19:45667400-45668600	Enhancers	Fetal Muscle Leg	muscle
48	chr19:45667400-45668600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr19:45667400-45668600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr19:45667400-45669000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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