Variant report

Variant	rs73546050
Chromosome Location	chr19:39830506-39830507
allele	G/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	CTCF	chr19:39830453-39830514	GM10248	blood:	n/a	n/a
2	CTCF	chr19:39830410-39830507	GM19239	blood:	n/a	n/a
3	CTCF	chr19:39830453-39830519	HepG2	liver:	n/a	n/a
4	HNF4G	chr19:39830346-39830558	HepG2	liver:	n/a	chr19:39830438-39830453

No.	Distal block	Cell Line	Cell type
1	chr19:39826587..39828135-chr19:39829547..39831242,2	K562	blood:
2	chr19:39829936..39834375-chr19:39901478..39904741,5	MCF-7	breast:
3	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:
4	chr19:39822373..39824358-chr19:39828655..39830757,2	MCF-7	breast:

Variant related genes	Relation type
SAMD4B	TF binding region
GMFG	TF binding region
ENSG00000090924	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs41275744	0.89[ASN][1000 genomes]
rs55874141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56190851	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56388054	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57310698	0.94[ASN][1000 genomes]
rs57850430	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73546038	0.84[AFR][1000 genomes]
rs73546046	1.00[ASN][1000 genomes]
rs73546077	1.00[AMR][1000 genomes]
rs73546088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73547912	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73930730	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8101598	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8102889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
4	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
6	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39818600-39831600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr19:39823800-39831200	Weak transcription	A549	lung
3	chr19:39826400-39831400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:39826400-39831400	Weak transcription	Brain Angular Gyrus	brain
5	chr19:39826400-39831400	Weak transcription	Brain Anterior Caudate	brain
6	chr19:39826400-39831400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:39826400-39831400	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:39826600-39830600	Weak transcription	Liver	Liver
9	chr19:39826600-39830600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:39826600-39830600	Weak transcription	Fetal Intestine Large	intestine
11	chr19:39826600-39830800	Weak transcription	Lung	lung
12	chr19:39826600-39831400	Weak transcription	Small Intestine	intestine
13	chr19:39826600-39831600	Weak transcription	Esophagus	oesophagus
14	chr19:39826800-39831000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:39826800-39831200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr19:39826800-39831400	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:39826800-39831400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr19:39826800-39831400	Weak transcription	Left Ventricle	heart
19	chr19:39826800-39831400	Weak transcription	Right Ventricle	heart
20	chr19:39826800-39831600	Weak transcription	Right Atrium	heart
21	chr19:39827000-39831200	Weak transcription	Placenta	Placenta
22	chr19:39827000-39831200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:39827000-39831200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:39827000-39831400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:39827000-39831400	Enhancers	Fetal Thymus	thymus
26	chr19:39827000-39831400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:39827000-39831400	Weak transcription	NHLF	lung
28	chr19:39827400-39831200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:39827400-39831400	Weak transcription	HUVEC	blood vessel
30	chr19:39827600-39831200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:39828400-39830600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr19:39828400-39831200	Weak transcription	HSMM	muscle
33	chr19:39828400-39831400	Weak transcription	Spleen	Spleen
34	chr19:39828600-39830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:39828600-39830800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:39828600-39831200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:39828600-39831200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39828600-39831200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:39828600-39831600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:39828800-39830600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr19:39828800-39830600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:39829200-39830600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39829200-39831200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:39829200-39831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:39829200-39831200	Weak transcription	Adipose Nuclei	Adipose
46	chr19:39829200-39831400	Weak transcription	Aorta	Aorta
47	chr19:39829200-39831400	Weak transcription	GM12878-XiMat	blood
48	chr19:39829200-39831400	Weak transcription	Hela-S3	cervix
49	chr19:39829400-39831200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:39829400-39831200	Weak transcription	Primary B cells from peripheral blood	blood

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