Variant report

Variant	rs73943603
Chromosome Location	chr19:47552695-47552696
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	EP300	chr19:47552613-47552901	Hela-S3	cervix:	n/a	chr19:47552687-47552697
2	TEAD4	chr19:47552658-47552954	H1-hESC	embryonic stem cell:	n/a	chr19:47552759-47552768
3	STAT3	chr19:47552610-47552881	MCF10A-Er-Src	breast:	n/a	chr19:47552756-47552764
4	MAFK	chr19:47552632-47552864	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr19:47552600-47552842	MCF10A-Er-Src	breast:	n/a	chr19:47552756-47552764
6	RFX5	chr19:47552612-47552904	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr19:47552635-47552938	Hela-S3	cervix:	n/a	chr19:47552756-47552764
8	RCOR1	chr19:47552587-47552969	Hela-S3	cervix:	n/a	n/a
9	SIX5	chr19:47551065-47552841	A549	lung:	n/a	chr19:47552148-47552162 chr19:47552149-47552158 chr19:47552151-47552160 chr19:47552154-47552163

No.	Distal block	Cell Line	Cell type
1	chr19:47550175..47552727-chr19:47729479..47731915,2	MCF-7	breast:
2	chr19:47521811..47526741-chr19:47550453..47554269,5	K562	blood:
3	chr19:47551339..47553570-chr19:47632652..47634525,2	MCF-7	breast:
4	chr19:47290385..47292241-chr19:47550652..47552913,2	K562	blood:
5	chr19:47537595..47541132-chr19:47548303..47552925,5	K562	blood:
6	chr19:47550333..47554198-chr19:47612165..47616505,8	K562	blood:
7	chr19:47551385..47554234-chr19:47614928..47616660,2	MCF-7	breast:
8	chr19:47549666..47554198-chr19:47613838..47618039,7	K562	blood:
9	chr19:47551143..47553326-chr19:47633296..47636151,3	K562	blood:
10	chr19:47539124..47541192-chr19:47549065..47553004,4	MCF-7	breast:

Variant related genes	Relation type
TMEM160	TF binding region
ENSG00000265134	Chromatin interaction
ENSG00000130749	Chromatin interaction
ENSG00000130751	Chromatin interaction
ENSG00000105281	Chromatin interaction
ENSG00000142230	Chromatin interaction
ENSG00000105327	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs73940802	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3346722	chr19:46779000-47555828	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
2	esv3319153	chr19:46779004-47555796	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
3	esv3319154	chr19:46779004-47555796	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
4	esv3397605	chr19:46779033-47555776	Flanking Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
5	nsv917664	chr19:47482403-48177720	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
6	nsv912192	chr19:47499031-47562123	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv912193	chr19:47519134-47562123	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv912194	chr19:47540859-47562123	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv912195	chr19:47540859-47569003	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:47550400-47552800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:47550400-47552800	Active TSS	HSMM	muscle
3	chr19:47550600-47552800	Active TSS	NHDF-Ad	bronchial
4	chr19:47550600-47553000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:47550600-47553000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:47550600-47553000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:47550800-47552800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:47550800-47552800	Active TSS	Colonic Mucosa	Colon
9	chr19:47551000-47553000	Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr19:47551200-47552800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:47551600-47552800	Active TSS	Stomach Smooth Muscle	stomach
12	chr19:47551800-47552800	Active TSS	Primary B cells from cord blood	blood
13	chr19:47551800-47552800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr19:47551800-47561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:47552000-47552800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr19:47552000-47558600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:47552200-47552800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:47552200-47553200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:47552200-47568200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:47552400-47552800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:47552400-47552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:47552400-47552800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr19:47552400-47552800	Weak transcription	Thymus	Thymus
24	chr19:47552400-47553000	Flanking Active TSS	Dnd41	blood
25	chr19:47552400-47553200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:47552600-47552800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr19:47552600-47552800	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:47552600-47552800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr19:47552600-47552800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:47552600-47552800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:47552600-47552800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr19:47552600-47552800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:47552600-47552800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr19:47552600-47552800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:47552600-47552800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:47552600-47552800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:47552600-47552800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr19:47552600-47552800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr19:47552600-47552800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:47552600-47552800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:47552600-47552800	Enhancers	Colon Smooth Muscle	Colon
42	chr19:47552600-47552800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr19:47552600-47552800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr19:47552600-47552800	Flanking Active TSS	A549	lung
45	chr19:47552600-47552800	Flanking Active TSS	HSMMtube	muscle
46	chr19:47552600-47552800	Enhancers	NHEK	skin
47	chr19:47552600-47552800	Enhancers	NHLF	lung
48	chr19:47552600-47552800	Flanking Active TSS	Osteobl	bone
49	chr19:47552600-47553000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr19:47552600-47553000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links