Variant report

Variant	rs73545999
Chromosome Location	chr19:40504423-40504424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40475223..40478471-chr19:40501440..40504433,4	MCF-7	breast:
2	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
3	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF546-1	chr19:40504155-40504457	NONHSAT066333

Variant related genes	Relation type
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs450095	0.87[EUR][1000 genomes]
rs55724336	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59307138	1.00[EUR][1000 genomes]
rs60037732	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61655884	0.87[EUR][1000 genomes]
rs7245925	0.87[EUR][1000 genomes]
rs7249514	1.00[EUR][1000 genomes]
rs7250763	1.00[EUR][1000 genomes]
rs7252478	0.85[AFR][1000 genomes]
rs7255186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73543966	1.00[EUR][1000 genomes]
rs73545987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73547626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73547631	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73547632	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73547672	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549807	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549809	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549848	1.00[EUR][1000 genomes]
rs73551667	0.87[EUR][1000 genomes]
rs73551692	0.87[EUR][1000 genomes]
rs8106043	0.87[EUR][1000 genomes]
rs8106753	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40503000-40504800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:40503600-40504600	Enhancers	HMEC	breast
3	chr19:40503600-40504600	Enhancers	NHDF-Ad	bronchial
4	chr19:40503600-40504600	Enhancers	NHEK	skin
5	chr19:40503600-40505000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:40503600-40507000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:40503600-40507400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:40503600-40511800	Weak transcription	Ovary	ovary
9	chr19:40503600-40511800	Weak transcription	Spleen	Spleen
10	chr19:40503600-40512000	Weak transcription	Esophagus	oesophagus
11	chr19:40503600-40512400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:40503600-40513000	Weak transcription	Placenta	Placenta
13	chr19:40503600-40514000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:40503600-40519200	Weak transcription	Small Intestine	intestine
15	chr19:40503800-40504600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40503800-40504600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:40503800-40504600	Enhancers	NHLF	lung
18	chr19:40503800-40504800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:40503800-40505200	Enhancers	HSMM	muscle
20	chr19:40503800-40505600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:40503800-40505800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:40503800-40506800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:40503800-40511000	Weak transcription	Right Atrium	heart
24	chr19:40503800-40511400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:40503800-40512000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr19:40503800-40512000	Weak transcription	Lung	lung
27	chr19:40503800-40512200	Weak transcription	Aorta	Aorta
28	chr19:40503800-40512200	Weak transcription	Gastric	stomach
29	chr19:40503800-40512400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:40503800-40512400	Weak transcription	Brain Angular Gyrus	brain
31	chr19:40503800-40512800	Weak transcription	Brain Germinal Matrix	brain
32	chr19:40503800-40513000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:40503800-40513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:40503800-40513200	Weak transcription	Fetal Intestine Large	intestine
35	chr19:40503800-40513400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:40503800-40513400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:40503800-40513400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr19:40503800-40513800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr19:40503800-40513800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:40503800-40513800	Weak transcription	Fetal Stomach	stomach
41	chr19:40503800-40514000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:40503800-40514000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:40503800-40514400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:40503800-40514600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:40503800-40514600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:40503800-40516000	Weak transcription	Fetal Intestine Small	intestine
47	chr19:40504000-40504600	Enhancers	Primary T cells from cord blood	blood
48	chr19:40504000-40504800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:40504000-40505200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:40504000-40505400	Weak transcription	Brain Anterior Caudate	brain

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