Variant report

Variant	rs73550461
Chromosome Location	chr19:40325042-40325043
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	MTA3	chr19:40322859-40325426	GM12878	blood:	n/a	n/a
2	SIN3A	chr19:40323786-40325203	H1-hESC	embryonic stem cell:	n/a	chr19:40324858-40324867
3	ELF1	chr19:40323743-40325117	GM12878	blood:	n/a	chr19:40323990-40324002
4	USF2	chr19:40324130-40325172	H1-hESC	embryonic stem cell:	n/a	chr19:40324856-40324867 chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324855-40324868 chr19:40324520-40324536 chr19:40324857-40324866 chr19:40324528-40324544
5	EP300	chr19:40324038-40325677	A549	lung:	n/a	n/a
6	USF1	chr19:40324500-40325065	GM12878	blood:	n/a	chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324855-40324868 chr19:40324520-40324536 chr19:40324857-40324866 chr19:40324528-40324544
7	ELF1	chr19:40324020-40325132	MCF-7	breast:	n/a	n/a
8	POU2F2	chr19:40324029-40325143	GM12891	blood:	n/a	chr19:40324229-40324241 chr19:40324843-40324855
9	USF1	chr19:40324632-40325077	GM12878	blood:	n/a	chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324855-40324868 chr19:40324857-40324866
10	TBL1XR1	chr19:40324134-40325221	K562	blood:	n/a	n/a
11	POLR2A	chr19:40323851-40325236	H1-neurons	neurons:	n/a	n/a
12	USF1	chr19:40323916-40325224	ECC-1	luminal epithelium:	n/a	chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324085-40324101 chr19:40324855-40324868 chr19:40324520-40324536 chr19:40324857-40324866 chr19:40324528-40324544
13	MAZ	chr19:40324066-40325043	Hela-S3	cervix:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
14	YY1	chr19:40324166-40325114	SK-N-SH	brain:	n/a	chr19:40324774-40324796 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40324891-40324899 chr19:40324878-40324900 chr19:40324785-40324793
15	ATF3	chr19:40324107-40325326	A549	lung:	n/a	chr19:40324649-40324658 chr19:40324857-40324866
16	MAX	chr19:40323793-40325208	ECC-1	luminal epithelium:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
17	POLR2A	chr19:40323486-40325688	GM12878	blood:	n/a	n/a
18	ELF1	chr19:40324039-40325229	A549	lung:	n/a	n/a
19	POLR2A	chr19:40323959-40325154	GM12892	blood:	n/a	n/a
20	MAX	chr19:40324127-40325099	Hela-S3	cervix:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
21	MAX	chr19:40323896-40325337	K562	blood:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
22	POLR2A	chr19:40324081-40325153	GM12891	blood:	n/a	n/a
23	TAF1	chr19:40324427-40325146	H1-neurons	neurons:	n/a	n/a
24	SIN3AK20	chr19:40324018-40325305	A549	lung:	n/a	n/a
25	POLR2A	chr19:40324061-40325336	K562	blood:	n/a	n/a
26	POLR2A	chr19:40323939-40325209	U87	brain:	n/a	n/a
27	YY1	chr19:40323868-40325090	SK-N-SH_RA	brain:	n/a	chr19:40323986-40324000 chr19:40324774-40324796 chr19:40323974-40323993 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40323969-40323991 chr19:40324891-40324899 chr19:40323979-40323991 chr19:40324878-40324900 chr19:40324105-40324114 chr19:40323936-40323947 chr19:40324785-40324793
28	MYC	chr19:40324491-40325059	HUVEC	blood vessel:	n/a	chr19:40324544-40324554 chr19:40324857-40324866 chr19:40324812-40324821
29	NR2F2	chr19:40324717-40325157	K562	blood:	n/a	n/a
30	CEBPB	chr19:40324162-40325272	A549	lung:	n/a	chr19:40324353-40324361
31	POLR2A	chr19:40323967-40325128	MCF-7	breast:	n/a	n/a
32	REST	chr19:40324103-40325382	A549	lung:	n/a	chr19:40324393-40324413 chr19:40324106-40324119 chr19:40324521-40324534
33	POLR2A	chr19:40323839-40325238	Hela-S3	cervix:	n/a	n/a
34	YY1	chr19:40323749-40325188	GM12878	blood:	n/a	chr19:40323986-40324000 chr19:40324774-40324796 chr19:40323974-40323993 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40323969-40323991 chr19:40324891-40324899 chr19:40323979-40323991 chr19:40324878-40324900 chr19:40324105-40324114 chr19:40323936-40323947 chr19:40324785-40324793
35	PAX5	chr19:40324515-40325086	GM12878	blood:	n/a	n/a
36	MAX	chr19:40323904-40325205	H1-hESC	embryonic stem cell:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
37	MAZ	chr19:40323889-40325096	GM12878	blood:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
38	NR2F2	chr19:40324037-40325337	K562	blood:	n/a	n/a
39	PML	chr19:40324283-40325232	K562	blood:	n/a	n/a
40	ZBTB33	chr19:40324127-40325412	A549	lung:	n/a	n/a
41	POLR2A	chr19:40323974-40325284	HUVEC	blood vessel:	n/a	n/a
42	MYC	chr19:40324033-40325046	MCF-7	breast:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
43	POLR2A	chr19:40323939-40325230	U87	brain:	n/a	n/a
44	POLR2A	chr19:40323785-40325466	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr19:40324068-40325223	GM12891	blood:	n/a	n/a
46	SP1	chr19:40324635-40325166	GM12878	blood:	n/a	chr19:40324826-40324836 chr19:40324826-40324840 chr19:40324825-40324837 chr19:40324825-40324837 chr19:40324827-40324836
47	E2F4	chr19:40324175-40325208	K562	blood:	n/a	chr19:40324909-40324918 chr19:40324352-40324361
48	GABPA	chr19:40324090-40325142	A549	lung:	n/a	chr19:40324881-40324890 chr19:40324105-40324114 chr19:40324985-40324999 chr19:40324905-40324919 chr19:40324908-40324919 chr19:40324910-40324919 chr19:40324908-40324922
49	POLR2A	chr19:40323955-40325109	A549	lung:	n/a	n/a
50	NFYB	chr19:40324070-40325121	GM12878	blood:	n/a	chr19:40324349-40324361 chr19:40324347-40324362 chr19:40324350-40324365 chr19:40324350-40324364 chr19:40324352-40324362 chr19:40324350-40324365

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40324993-40325043	GM12878	blood:	n/a
2	chr19:40324993-40325043	A549	lung:	n/a
3	chr19:40324993-40325043	T-47D	breast:	n/a
4	chr19:40324993-40325043	AG10803	skin:	n/a
5	chr19:40324993-40325043	SK-N-SH	brain:	n/a
6	chr19:40324993-40325043	PrEC	prostate:	n/a
7	chr19:40324993-40325043	ProgFib	skin:	n/a
8	chr19:40324993-40325043	HEEpiC	esophagus:	n/a
9	chr19:40324993-40325043	AG04449	skin:	fetal
10	chr19:40324993-40325043	NHDF-neo	bronchial:	n/a
11	chr19:40324993-40325043	RPTEC	kidney:	n/a
12	chr19:40324993-40325043	NT2-D1	testis:	n/a
13	chr19:40324993-40325043	BE2_C	brain:	n/a
14	chr19:40324993-40325043	PANC-1	pancreas:	n/a
15	chr19:40324993-40325043	SAEC	small airway:	n/a
16	chr19:40324993-40325043	HRPEpiC	eye:	n/a
17	chr19:40324993-40325043	Caco-2	colon:	n/a
18	chr19:40324993-40325043	NH-A	brain:	n/a
19	chr19:40324993-40325043	CMK	blood:	n/a
20	chr19:40324993-40325043	SK-N-MC	brain:	n/a
21	chr19:40324993-40325043	SKMC	muscle:	n/a
22	chr19:40324993-40325043	MCF10A-Er-Src	breast:	n/a
23	chr19:40324993-40325043	SK-N-SH_RA	brain:	n/a
24	chr19:40324993-40325043	HCPEpiC	choroid plexus:	n/a
25	chr19:40324993-40325043	GM12892	blood:	n/a
26	chr19:40324993-40325043	GM12891	blood:	n/a
27	chr19:40324993-40325043	HCM	heart:	n/a
28	chr19:40324993-40325043	HCT-116	colon:	n/a
29	chr19:40324993-40325043	HRE	kidney:	n/a
30	chr19:40324993-40325043	GM19239	blood:	n/a
31	chr19:40324993-40325043	MCF-7	breast:	n/a
32	chr19:40324993-40325043	Jurkat	blood:	n/a
33	chr19:40324993-40325043	Hela-S3	cervix:	n/a
34	chr19:40324993-40325043	HAEpiC	amniotic membrane:	n/a
35	chr19:40324993-40325043	AoSMC	blood vessel:	n/a
36	chr19:40324993-40325043	AG09319	gingival:	n/a
37	chr19:40324993-40325043	BJ	skin:	n/a
38	chr19:40324993-40325043	HNPCEpiC	eye:	n/a
39	chr19:40324993-40325043	HEK293	kidney:	embryo
40	chr19:40324993-40325043	AG09309	skin:	n/a
41	chr19:40324993-40325043	HCF	heart:	n/a
42	chr19:40324993-40325043	Hepatocyte	liver:	n/a
43	chr19:40324993-40325043	ovcar-3	ovarian:	n/a
44	chr19:40324993-40325043	HPAEpiC	pulmonary alveolar:	n/a
45	chr19:40324993-40325043	NB4	blood:	n/a
46	chr19:40324993-40325043	LNCaP	prostate:	n/a
47	chr19:40324993-40325043	U87	brain:	n/a
48	chr19:40324993-40325043	AG04450	lung:	fetal
49	chr19:40324993-40325043	HRCEpiC	kidney:	n/a
50	chr19:40324993-40325043	HUVEC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40323585..40327109-chr19:40328017..40332842,7	MCF-7	breast:
2	chr19:40318662..40321360-chr19:40322185..40325984,6	MCF-7	breast:
3	chr19:40324934..40327706-chr19:40474760..40476442,2	K562	blood:
4	chr19:40323873..40328898-chr19:40330848..40333267,4	MCF-7	breast:
5	chr19:39926032..39928483-chr19:40324303..40326455,2	MCF-7	breast:
6	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
7	chr19:39900130..39902222-chr19:40323529..40326104,2	MCF-7	breast:
8	chr19:40323895..40326074-chr19:40326895..40329517,2	MCF-7	breast:
9	chr19:40322842..40325581-chr19:40335629..40338491,6	MCF-7	breast:
10	chr19:40321676..40323398-chr19:40323422..40325295,2	MCF-7	breast:

Variant related genes	Relation type
DYRK1B	TF binding region
DYRK1B	CpG island
ENSG00000266559	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000105193	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]
rs73550456	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40318000-40331800	Strong transcription	HepG2	liver
2	chr19:40322600-40325600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:40323600-40325400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:40323800-40325200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:40323800-40325200	Active TSS	Colon Smooth Muscle	Colon
6	chr19:40324200-40325200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:40324400-40325200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:40324400-40325200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
9	chr19:40324400-40325200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:40324800-40325200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:40324800-40325200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:40324800-40325200	Flanking Active TSS	Colonic Mucosa	Colon
13	chr19:40324800-40325200	Flanking Active TSS	Esophagus	oesophagus
14	chr19:40324800-40325200	Transcr. at gene 5' and 3'	Placenta	Placenta
15	chr19:40324800-40325200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:40324800-40325200	Flanking Active TSS	Stomach Mucosa	stomach
17	chr19:40324800-40325200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr19:40324800-40325400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:40324800-40325400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:40324800-40325400	Transcr. at gene 5' and 3'	NHEK	skin
21	chr19:40324800-40325600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:40324800-40325600	Genic enhancers	HMEC	breast
23	chr19:40324800-40327000	Weak transcription	Aorta	Aorta
24	chr19:40324800-40327000	Weak transcription	Ovary	ovary
25	chr19:40324800-40327000	Weak transcription	Small Intestine	intestine
26	chr19:40324800-40327200	Weak transcription	Psoas Muscle	Psoas
27	chr19:40324800-40327400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:40324800-40336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:40325000-40325200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
30	chr19:40325000-40325200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
31	chr19:40325000-40325200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:40325000-40325200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:40325000-40325200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
34	chr19:40325000-40325200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
35	chr19:40325000-40325200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:40325000-40325200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
37	chr19:40325000-40325200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
38	chr19:40325000-40325200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
39	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:40325000-40325200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:40325000-40325200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
45	chr19:40325000-40325200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:40325000-40325200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
48	chr19:40325000-40325200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:40325000-40325200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
50	chr19:40325000-40325200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

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