Variant report

Variant	rs73549848
Chromosome Location	chr19:40597520-40597521
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	FOSL2	chr19:40596072-40597598	A549	lung:	n/a	chr19:40596194-40596206
2	HCFC1	chr19:40595389-40597742	Hela-S3	cervix:	n/a	n/a
3	EP300	chr19:40596867-40597595	K562	blood:	n/a	n/a
4	MXI1	chr19:40595191-40597631	SK-N-SH	brain:	n/a	n/a
5	SIX5	chr19:40596444-40597604	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40501950..40503610-chr19:40595158..40598072,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF546-3	chr19:40596661-40600313	ENSG00000269296.1

Variant related genes	Relation type
ENSG00000269749	TF binding region
ZNF780A	TF binding region
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs450095	0.87[EUR][1000 genomes]
rs55724336	1.00[EUR][1000 genomes]
rs59307138	1.00[EUR][1000 genomes]
rs60037732	1.00[EUR][1000 genomes]
rs61655884	0.87[EUR][1000 genomes]
rs7245925	0.87[EUR][1000 genomes]
rs7249514	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250763	1.00[EUR][1000 genomes]
rs7255186	1.00[EUR][1000 genomes]
rs73543966	1.00[EUR][1000 genomes]
rs73545987	1.00[EUR][1000 genomes]
rs73545999	1.00[EUR][1000 genomes]
rs73547626	1.00[EUR][1000 genomes]
rs73547631	1.00[EUR][1000 genomes]
rs73547632	0.89[EUR][1000 genomes]
rs73547672	1.00[EUR][1000 genomes]
rs73549807	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73549809	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551667	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73551692	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8106043	0.87[EUR][1000 genomes]
rs8106753	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv2488	chr19:40593818-40631406	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40595400-40597600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:40595400-40597600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:40595400-40597600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:40595400-40597600	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:40595600-40597600	Active TSS	Fetal Intestine Large	intestine
6	chr19:40595600-40597600	Active TSS	Fetal Kidney	kidney
7	chr19:40595800-40597600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:40595800-40597600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:40595800-40597600	Active TSS	Colonic Mucosa	Colon
10	chr19:40595800-40597600	Active TSS	NHDF-Ad	bronchial
11	chr19:40595800-40597800	Active TSS	GM12878-XiMat	blood
12	chr19:40596000-40597600	Active TSS	Brain Anterior Caudate	brain
13	chr19:40596000-40597600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr19:40596000-40597600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:40596200-40597600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:40596200-40597600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:40596200-40597600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:40596200-40597600	Active TSS	Brain Substantia Nigra	brain
19	chr19:40596200-40597600	Active TSS	Hela-S3	cervix
20	chr19:40596200-40597800	Active TSS	HMEC	breast
21	chr19:40596400-40597600	Active TSS	NHEK	skin
22	chr19:40596600-40597600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:40597000-40597600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:40597000-40597600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:40597000-40597600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:40597000-40597600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr19:40597000-40597600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr19:40597000-40597600	Flanking Active TSS	Liver	Liver
29	chr19:40597000-40597600	Flanking Active TSS	Dnd41	blood
30	chr19:40597200-40597600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:40597200-40597600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:40597200-40597600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr19:40597200-40597600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr19:40597200-40597600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr19:40597200-40597600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:40597200-40597600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr19:40597200-40597600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr19:40597200-40597600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:40597200-40597600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr19:40597200-40597600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:40597200-40597600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:40597200-40597600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr19:40597200-40597600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr19:40597200-40597600	Flanking Active TSS	A549	lung
45	chr19:40597200-40597600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr19:40597200-40597600	Flanking Active TSS	NHLF	lung
47	chr19:40597200-40597600	Flanking Active TSS	Osteobl	bone
48	chr19:40597400-40597600	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:40597400-40597600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr19:40597400-40597600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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