Variant report

Variant	rs73547993
Chromosome Location	chr19:39924466-39924467
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	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
2	POLR2A	chr19:39924388-39924757	K562	blood:	n/a	n/a
3	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
5	JUND	chr19:39920490-39925442	A549	lung:	n/a	chr19:39921458-39921466 chr19:39924892-39924906 chr19:39921457-39921466 chr19:39921456-39921467 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467 chr19:39922370-39922379 chr19:39922373-39922382 chr19:39922371-39922380
6	POLR2A	chr19:39920391-39924937	HepG2	liver:	n/a	n/a
7	MTA3	chr19:39924185-39924737	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:39922557-39925396	K562	blood:	n/a	n/a
9	ZBTB33	chr19:39923756-39924473	K562	blood:	n/a	n/a
10	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
11	CHD1	chr19:39922434-39927571	IMR90	lung:	n/a	chr19:39927410-39927420
12	SP1	chr19:39924216-39924545	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:39924062-39925198	K562	blood:	n/a	n/a
14	TCF7L2	chr19:39923094-39925387	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:39920942-39925617	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:39920975-39927064	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr19:39920712-39925660	IMR90	lung:	n/a	n/a
19	POLR2A	chr19:39922355-39925341	SK-N-SH	brain:	n/a	n/a
20	BCL3	chr19:39922482-39925602	A549	lung:	n/a	chr19:39924869-39924878
21	POLR2A	chr19:39921015-39927381	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:39921127-39925489	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:39923863-39925119	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:39922588-39925489	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:39922723-39925532	K562	blood:	n/a	n/a
26	HEY1	chr19:39923993-39924732	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
28	POLR2A	chr19:39923976-39924498	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:39920992-39925485	GM12891	blood:	n/a	n/a
30	REST	chr19:39920516-39925106	PANC-1	pancreas:	n/a	chr19:39924867-39924880
31	POLR2A	chr19:39921169-39925654	K562	blood:	n/a	n/a
32	POLR2A	chr19:39922383-39925441	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:39921059-39925766	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
35	POLR2A	chr19:39924223-39924492	A549	lung:	n/a	n/a
36	POLR2A	chr19:39921027-39924615	A549	lung:	n/a	n/a
37	CTCF	chr19:39924174-39924501	T-47D	breast:	n/a	n/a
38	POLR2A	chr19:39921064-39925450	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr19:39923887-39924589	A549	lung:	n/a	n/a
40	POLR2A	chr19:39922700-39925056	GM18505	blood:	n/a	n/a
41	POLR2A	chr19:39922720-39925026	GM19193	blood:	n/a	n/a
42	POLR2A	chr19:39921143-39925465	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:39922601-39925454	GM12891	blood:	n/a	n/a
44	POLR2A	chr19:39922392-39925452	H1-hESC	embryonic stem cell:	n/a	n/a
45	EP300	chr19:39924067-39927364	A549	lung:	n/a	chr19:39925993-39926009 chr19:39927161-39927175
46	SIN3AK20	chr19:39920798-39927887	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr19:39920903-39927409	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr19:39920869-39927284	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr19:39921038-39925111	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr19:39922546-39925580	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39924275..39926732-chr19:39958030..39960191,3	K562	blood:
2	chr19:39875302..39877706-chr19:39923653..39926638,3	MCF-7	breast:
3	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
4	chr17:7475764..7476400-chr19:39923946..39924715,2	Hela-S3	cervix:
5	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
6	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:

Variant related genes	Relation type
SUPT5H	TF binding region
RPS16	TF binding region
ENSG00000176396	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000161960	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10413140	1.00[AMR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes]
rs61569178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549906	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549912	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549922	1.00[AMR][1000 genomes]
rs73549928	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551839	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	0.91[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	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 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	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39919600-39925000	Weak transcription	Right Atrium	heart
3	chr19:39919800-39924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39921200-39924600	Strong transcription	Brain Germinal Matrix	brain
5	chr19:39921200-39924800	Strong transcription	Brain Hippocampus Middle	brain
6	chr19:39921600-39924800	Strong transcription	Brain Inferior Temporal Lobe	brain
7	chr19:39921600-39925200	Strong transcription	Thymus	Thymus
8	chr19:39921600-39925600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:39921800-39924600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:39921800-39924600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:39921800-39924600	Strong transcription	Fetal Stomach	stomach
12	chr19:39922000-39924800	Strong transcription	Fetal Intestine Small	intestine
13	chr19:39922000-39924800	Weak transcription	Stomach Mucosa	stomach
14	chr19:39922000-39925200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:39922200-39924600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr19:39922200-39924800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:39922200-39924800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:39922600-39924600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:39922600-39924600	Strong transcription	Liver	Liver
20	chr19:39922600-39925200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:39922800-39924600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:39922800-39924600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:39922800-39924600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr19:39922800-39924600	Strong transcription	Osteobl	bone
25	chr19:39922800-39924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39922800-39924800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:39922800-39924800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:39922800-39924800	Strong transcription	Fetal Intestine Large	intestine
29	chr19:39922800-39925200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39923000-39924600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:39923000-39924600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:39923000-39924600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:39923000-39924600	Strong transcription	Brain Substantia Nigra	brain
34	chr19:39923000-39924600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr19:39923000-39924600	Strong transcription	Rectal Smooth Muscle	rectum
36	chr19:39923000-39924600	Strong transcription	HSMM	muscle
37	chr19:39923000-39924600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr19:39923000-39924600	Strong transcription	NH-A	brain
39	chr19:39923000-39924800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39923000-39924800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:39923000-39924800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr19:39923000-39924800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:39923000-39925000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:39923000-39925200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:39923200-39924600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr19:39923200-39924600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:39923200-39924600	Strong transcription	Fetal Lung	lung
48	chr19:39923200-39924600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:39923200-39924600	Strong transcription	Small Intestine	intestine
50	chr19:39923200-39924600	Strong transcription	HMEC	breast

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