Variant report

Variant	rs73550456
Chromosome Location	chr19:40323066-40323067
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	MTA3	chr19:40322859-40325426	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40323006-40323308	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT5A	chr19:40322793-40323784	GM12878	blood:	n/a	chr19:40322947-40322958 chr19:40323167-40323179 chr19:40323376-40323399
4	REST	chr19:40322858-40325508	PANC-1	pancreas:	n/a	chr19:40324393-40324413 chr19:40324106-40324119 chr19:40324521-40324534
5	SIN3AK20	chr19:40319989-40326136	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
7	RFX5	chr19:40323032-40325327	IMR90	lung:	n/a	chr19:40324377-40324386 chr19:40324304-40324321 chr19:40324310-40324319 chr19:40324375-40324391 chr19:40324373-40324388 chr19:40324307-40324322 chr19:40324376-40324390 chr19:40324374-40324388 chr19:40324308-40324322 chr19:40324353-40324362
8	POLR2A	chr19:40322919-40325645	SK-N-MC	brain:	n/a	n/a
9	RUNX3	chr19:40322728-40323549	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:40323016-40325236	A549	lung:	n/a	n/a
11	EBF1	chr19:40322867-40323377	GM12878	blood:	n/a	chr19:40323319-40323329 chr19:40323222-40323233
12	NFIC	chr19:40322952-40323751	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:40323058-40323367	Hela-S3	cervix:	n/a	n/a
14	RFX5	chr19:40322962-40323238	GM12878	blood:	n/a	n/a
15	RUNX3	chr19:40322753-40323488	GM12878	blood:	n/a	n/a
16	MAZ	chr19:40322780-40325468	IMR90	lung:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
17	POLR2A	chr19:40322985-40323415	HL-60	blood:	n/a	n/a
18	STAT5A	chr19:40323001-40323423	GM12878	blood:	n/a	chr19:40323167-40323179 chr19:40323376-40323399
19	EBF1	chr19:40322900-40323417	GM12878	blood:	n/a	chr19:40323319-40323329 chr19:40323222-40323233
20	EBF1	chr19:40322871-40323327	GM12878	blood:	n/a	chr19:40323222-40323233
21	RFX5	chr19:40322868-40325564	SK-N-SH	brain:	n/a	chr19:40324377-40324386 chr19:40324304-40324321 chr19:40324310-40324319 chr19:40324375-40324391 chr19:40324373-40324388 chr19:40324307-40324322 chr19:40324376-40324390 chr19:40324374-40324388 chr19:40324308-40324322 chr19:40324353-40324362

No.	Distal block	Cell Line	Cell type
1	chr19:40318662..40321360-chr19:40322185..40325984,6	MCF-7	breast:
2	chr19:40321676..40323398-chr19:40323422..40325295,2	MCF-7	breast:
3	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
4	chr19:40322842..40325581-chr19:40335629..40338491,6	MCF-7	breast:

Variant related genes	Relation type
DYRK1B	TF binding region
ENSG00000105204	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs56903549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57358879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57647975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57898836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58457062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59182107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61293883	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61520181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62106865	0.86[AFR][1000 genomes]
rs6508908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6508909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7251711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7258204	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73546653	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546697	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548515	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73548523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73550461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8102268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8110565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40312000-40323200	Strong transcription	A549	lung
2	chr19:40315800-40323400	Weak transcription	Right Atrium	heart
3	chr19:40315800-40323600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:40316000-40323200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:40316000-40323200	Strong transcription	NHEK	skin
6	chr19:40316200-40323400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:40318000-40331800	Strong transcription	HepG2	liver
8	chr19:40318200-40323200	Weak transcription	Small Intestine	intestine
9	chr19:40320600-40323200	Strong transcription	HMEC	breast
10	chr19:40320800-40323200	Weak transcription	Stomach Mucosa	stomach
11	chr19:40321000-40323200	Weak transcription	Colonic Mucosa	Colon
12	chr19:40321400-40323400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:40321400-40323800	Weak transcription	Aorta	Aorta
14	chr19:40321600-40323200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:40321600-40323400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:40321800-40323200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:40321800-40323400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:40321800-40323400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:40321800-40323600	Enhancers	Psoas Muscle	Psoas
20	chr19:40321800-40323800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
21	chr19:40322000-40323600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:40322200-40323200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:40322200-40323200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:40322200-40323200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr19:40322200-40323200	Enhancers	Fetal Heart	heart
26	chr19:40322200-40323200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
27	chr19:40322200-40323400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:40322200-40323400	Genic enhancers	NHLF	lung
29	chr19:40322400-40323200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:40322400-40323200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:40322400-40323200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:40322400-40323400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:40322400-40323400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr19:40322400-40323400	Enhancers	Pancreas	Pancrea
35	chr19:40322400-40323400	Enhancers	Right Ventricle	heart
36	chr19:40322400-40323600	Enhancers	Left Ventricle	heart
37	chr19:40322400-40323800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:40322600-40323200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:40322600-40323200	Enhancers	Brain Anterior Caudate	brain
40	chr19:40322600-40323200	Enhancers	Brain Hippocampus Middle	brain
41	chr19:40322600-40323200	Weak transcription	Ovary	ovary
42	chr19:40322600-40323200	Enhancers	Stomach Smooth Muscle	stomach
43	chr19:40322600-40323400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:40322600-40323600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:40322600-40323600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:40322600-40323600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:40322600-40323600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr19:40322600-40323800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:40322600-40325600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:40322800-40323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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