Variant report

Variant	rs73033380
Chromosome Location	chr19:39925621-39925622
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	POLR2A	chr19:39925540-39925988	A549	lung:	n/a	n/a
2	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
3	POLR2A	chr19:39925575-39925631	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
7	CHD1	chr19:39924942-39925688	GM12878	blood:	n/a	n/a
8	MXI1	chr19:39925603-39927602	SK-N-SH	brain:	n/a	n/a
9	CHD1	chr19:39922434-39927571	IMR90	lung:	n/a	chr19:39927410-39927420
10	JUND	chr19:39925554-39927180	A549	lung:	n/a	n/a
11	POLR2A	chr19:39920975-39927064	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr19:39920712-39925660	IMR90	lung:	n/a	n/a
14	POLR2A	chr19:39921015-39927381	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
16	SIN3AK20	chr19:39924841-39925791	A549	lung:	n/a	n/a
17	POLR2A	chr19:39921169-39925654	K562	blood:	n/a	n/a
18	REST	chr19:39924805-39925732	A549	lung:	n/a	chr19:39924867-39924880
19	MYC	chr19:39924499-39927878	A549	lung:	n/a	n/a
20	POLR2A	chr19:39921059-39925766	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
22	POLR2A	chr19:39925586-39928296	HepG2	liver:	n/a	n/a
23	FOSL2	chr19:39925433-39927501	A549	lung:	n/a	chr19:39927413-39927422
24	EP300	chr19:39924067-39927364	A549	lung:	n/a	chr19:39925993-39926009 chr19:39927161-39927175
25	POLR2A	chr19:39925463-39925803	SK-N-SH	brain:	n/a	n/a
26	SIN3AK20	chr19:39920798-39927887	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr19:39920903-39927409	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr19:39920869-39927284	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:39925525-39925782	Hela-S3	cervix:	n/a	n/a
30	REST	chr19:39924537-39925800	A549	lung:	n/a	chr19:39924867-39924880
31	POLR2A	chr19:39925593-39925760	A549	lung:	n/a	n/a
32	ETS1	chr19:39924145-39925749	A549	lung:	n/a	n/a
33	POLR2A	chr19:39925452-39925808	HepG2	liver:	n/a	n/a
34	POLR2A	chr19:39921047-39927386	GM12892	blood:	n/a	n/a
35	POLR2A	chr19:39925141-39927033	K562	blood:	n/a	n/a
36	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
37	BCL3	chr19:39922499-39927500	A549	lung:	n/a	chr19:39926713-39926722 chr19:39927161-39927170 chr19:39926564-39926577 chr19:39925991-39926000 chr19:39924869-39924878
38	POLR2A	chr19:39921176-39925804	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:39920886-39928028	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr19:39920434-39927060	HUVEC	blood vessel:	n/a	n/a
41	REST	chr19:39925510-39927924	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr19:39921020-39925814	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:39925587-39925775	A549	lung:	n/a	n/a
44	POLR2A	chr19:39920980-39927382	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr19:39925598-39925949	GM12878	blood:	n/a	n/a
46	HEY1	chr19:39922803-39925717	K562	blood:	n/a	n/a
47	SP1	chr19:39925080-39927318	A549	lung:	n/a	chr19:39925991-39926000 chr19:39926456-39926465 chr19:39926689-39926698 chr19:39926687-39926699 chr19:39926455-39926469 chr19:39925992-39926001
48	POLR2A	chr19:39925552-39925799	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr19:39925533-39925810	HL-60	blood:	n/a	n/a
50	POLR2A	chr19:39920968-39927110	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
2	chr19:39925083..39926660-chr19:39982191..39985073,2	K562	blood:
3	chr19:39924275..39926732-chr19:39958030..39960191,3	K562	blood:
4	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
5	chr19:39875302..39877706-chr19:39923653..39926638,3	MCF-7	breast:
6	chr19:39925059..39926909-chr6:27114877..27117589,2	MCF-7	breast:
7	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
8	chr19:39925068..39927999-chr19:40329043..40331985,2	K562	blood:
9	chr19:39832183..39834517-chr19:39925160..39926923,2	MCF-7	breast:
10	chr19:39925314..39927864-chr19:40336547..40338108,2	K562	blood:
11	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:
12	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
13	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
14	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:
15	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
16	chr19:39925075..39926642-chr19:40022135..40025107,3	K562	blood:

Variant related genes	Relation type
SUPT5H	TF binding region
RPS16	TF binding region
ENSG00000213922	TF binding region
ENSG00000105202	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000269246	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10408198	0.84[AMR][1000 genomes]
rs10410755	0.84[AMR][1000 genomes]
rs17627	0.90[EUR][1000 genomes]
rs62119738	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62120663	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120664	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62120667	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62120670	0.84[AMR][1000 genomes]
rs73035432	0.91[AFR][1000 genomes];0.85[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	chr19:39923200-39926200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr19:39923600-39926600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:39923800-39926400	Transcr. at gene 5' and 3'	A549	lung
5	chr19:39924200-39925800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr19:39924200-39926400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr19:39924400-39925800	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr19:39924600-39925800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
9	chr19:39924600-39925800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:39924600-39925800	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
11	chr19:39924600-39926000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39924600-39926200	Transcr. at gene 5' and 3'	NHEK	skin
13	chr19:39924600-39926400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
14	chr19:39924800-39925800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39924800-39925800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
16	chr19:39924800-39925800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
17	chr19:39925000-39925800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39925000-39925800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39925000-39925800	Enhancers	Right Atrium	heart
20	chr19:39925000-39926000	Enhancers	Small Intestine	intestine
21	chr19:39925000-39926600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39925000-39926600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
23	chr19:39925000-39927200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr19:39925200-39925800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
25	chr19:39925200-39925800	Flanking Active TSS	Fetal Heart	heart
26	chr19:39925200-39925800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
27	chr19:39925200-39925800	Transcr. at gene 5' and 3'	Lung	lung
28	chr19:39925200-39925800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr19:39925200-39926000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39925200-39926000	Enhancers	Brain Substantia Nigra	brain
31	chr19:39925200-39926000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr19:39925200-39926000	Enhancers	Spleen	Spleen
33	chr19:39925200-39927000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:39925200-39927400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr19:39925400-39925800	Genic enhancers	Primary B cells from cord blood	blood
36	chr19:39925400-39925800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:39925400-39925800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr19:39925400-39925800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:39925400-39925800	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr19:39925400-39925800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr19:39925400-39925800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr19:39925400-39925800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:39925400-39925800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr19:39925400-39925800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr19:39925400-39925800	Weak transcription	Left Ventricle	heart
46	chr19:39925400-39925800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr19:39925400-39925800	Flanking Active TSS	Stomach Mucosa	stomach
48	chr19:39925400-39925800	Flanking Active TSS	HSMM	muscle
49	chr19:39925400-39925800	Flanking Active TSS	HSMMtube	muscle
50	chr19:39925400-39926000	Flanking Active TSS	Primary T cells from cord blood	blood

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