Variant report

Variant	rs73044940
Chromosome Location	chr19:38892039-38892040
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	GATA3	chr19:38891796-38892196	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:38891621-38892723	HUVEC	blood vessel:	n/a	n/a
3	FOXA1	chr19:38891808-38892155	T-47D	breast:	n/a	chr19:38891992-38892004
4	FOXA1	chr19:38891791-38892127	HepG2	liver:	n/a	chr19:38891992-38892004
5	STAT3	chr19:38891835-38892065	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:38886771-38892156	PFSK-1	brain:	n/a	n/a
7	STAT3	chr19:38891956-38892156	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr19:38891235-38894621	A549	lung:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
9	FOS	chr19:38891922-38892149	MCF10A-Er-Src	breast:	n/a	n/a
10	FOXA1	chr19:38891815-38892150	T-47D	breast:	n/a	chr19:38891992-38892004
11	GATA2	chr19:38891821-38892151	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr19:38891811-38892463	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr19:38891762-38892117	T-47D	breast:	n/a	n/a
14	GATA3	chr19:38891972-38892048	SH-SY5Y	brain:	n/a	n/a
15	FOXA1	chr19:38891866-38892113	HepG2	liver:	n/a	chr19:38891992-38892004
16	POLR2A	chr19:38887005-38894478	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr19:38892002-38892061	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr19:38886848-38892855	PFSK-1	brain:	n/a	n/a
19	E2F4	chr19:38891944-38892323	MCF10A-Er-Src	breast:	n/a	n/a
20	FOXA2	chr19:38891898-38892090	HepG2	liver:	n/a	chr19:38891992-38892004
21	FOXA1	chr19:38891725-38892119	HepG2	liver:	n/a	chr19:38891992-38892004
22	ARID3A	chr19:38891923-38892096	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:38891873-38892425	HUVEC	blood vessel:	n/a	n/a
24	GATA3	chr19:38891734-38892151	T-47D	breast:	n/a	n/a
25	FOXA1	chr19:38891770-38892133	HepG2	liver:	n/a	chr19:38891992-38892004
26	POLR2A	chr19:38891948-38892122	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr19:38890306-38894281	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38890926..38893595-chr19:38978170..38979921,2	K562	blood:
2	chr19:38882154..38886821-chr19:38889933..38892699,4	MCF-7	breast:
3	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
4	chr19:38886501..38890187-chr19:38891290..38894154,6	MCF-7	breast:
5	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:
6	chr19:38891977..38893968-chr19:38915428..38917384,2	K562	blood:

Variant related genes	Relation type
FAM98C	TF binding region
ENSG00000188766	Chromatin interaction
ENSG00000267473	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11880532	0.84[AFR][1000 genomes]
rs12609878	0.87[AFR][1000 genomes]
rs2041221	0.82[AFR][1000 genomes]
rs2074981	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745955	0.81[EUR][1000 genomes]
rs61162240	0.87[AFR][1000 genomes]
rs73044923	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS 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	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
5	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38884800-38893200	Weak transcription	NH-A	brain
7	chr19:38885200-38893200	Weak transcription	HSMM	muscle
8	chr19:38885800-38893200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr19:38887000-38893200	Weak transcription	NHDF-Ad	bronchial
10	chr19:38887200-38892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38887200-38892400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:38887400-38893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:38887400-38893200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:38887400-38893200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:38887400-38893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:38887400-38893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:38887400-38893200	Weak transcription	NHEK	skin
18	chr19:38887600-38893200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:38887600-38893200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:38887600-38893200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:38887600-38893200	Weak transcription	NHLF	lung
22	chr19:38887800-38893200	Weak transcription	Osteobl	bone
23	chr19:38888000-38893200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:38888000-38893200	Weak transcription	Right Atrium	heart
25	chr19:38890200-38892200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:38891000-38893200	Enhancers	Placenta	Placenta
27	chr19:38891200-38893400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38891400-38892400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:38891400-38893200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:38891600-38893400	Enhancers	Stomach Mucosa	stomach
31	chr19:38892000-38893200	Weak transcription	A549	lung
32	chr19:38892000-38893200	Weak transcription	Hela-S3	cervix
33	chr19:38892000-38893200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links