Variant report

Variant	rs739846
Chromosome Location	chr19:19419071-19419072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19414752..19417045-chr19:19417211..19419630,2	MCF-7	breast:
2	chr19:19417598..19419748-chr19:19425185..19428061,2	MCF-7	breast:
3	chr19:19411942..19414744-chr19:19417979..19422177,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TM6SF2-2	chr19:19418030-19419666	NONHSAT063041

Variant related genes	Relation type
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10401969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668104	0.93[AFR][1000 genomes]
rs12459676	0.83[AFR][1000 genomes]
rs12979148	0.91[AFR][1000 genomes]
rs2023883	0.82[AFR][1000 genomes]
rs2240117	0.96[AFR][1000 genomes]
rs4808194	0.82[AFR][1000 genomes]
rs58542926	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72999033	0.90[EUR][1000 genomes]
rs73001065	0.83[EUR][1000 genomes]
rs8107974	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19384400-19430600	Weak transcription	Right Atrium	heart
2	chr19:19385400-19428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:19386200-19421000	Weak transcription	Stomach Mucosa	stomach
4	chr19:19386800-19428400	Strong transcription	Fetal Intestine Small	intestine
5	chr19:19388000-19429000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:19390800-19430000	Weak transcription	Psoas Muscle	Psoas
7	chr19:19397200-19420800	Weak transcription	NHDF-Ad	bronchial
8	chr19:19398000-19426800	Weak transcription	K562	blood
9	chr19:19402400-19427600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:19402400-19427800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:19402600-19427400	Strong transcription	Lung	lung
12	chr19:19402800-19427600	Strong transcription	Fetal Intestine Large	intestine
13	chr19:19402800-19428600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:19403000-19427800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr19:19403200-19421600	Strong transcription	Brain Germinal Matrix	brain
16	chr19:19403400-19423400	Strong transcription	Brain Hippocampus Middle	brain
17	chr19:19403400-19427800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:19403400-19428600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr19:19403600-19421800	Strong transcription	Adipose Nuclei	Adipose
20	chr19:19403800-19428200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr19:19404000-19427600	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:19404200-19427400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19404200-19429000	Strong transcription	Fetal Stomach	stomach
24	chr19:19404600-19427600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:19404600-19427600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:19404800-19428600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:19405000-19420800	Weak transcription	Fetal Kidney	kidney
28	chr19:19405000-19421000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:19405000-19427800	Strong transcription	Thymus	Thymus
30	chr19:19406200-19425200	Weak transcription	HSMM	muscle
31	chr19:19407000-19428200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:19408200-19428400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:19410800-19428400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:19410800-19428600	Strong transcription	Fetal Thymus	thymus
35	chr19:19411000-19421400	Strong transcription	Ovary	ovary
36	chr19:19411000-19421400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr19:19411000-19422600	Strong transcription	Placenta	Placenta
38	chr19:19411000-19427200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:19411000-19427800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr19:19411000-19428200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:19411200-19419200	Strong transcription	Pancreas	Pancrea
42	chr19:19411200-19419200	Strong transcription	Spleen	Spleen
43	chr19:19411200-19420200	Strong transcription	GM12878-XiMat	blood
44	chr19:19411200-19421600	Strong transcription	NHLF	lung
45	chr19:19411200-19421800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:19411200-19421800	Strong transcription	Esophagus	oesophagus
47	chr19:19411200-19423400	Strong transcription	Dnd41	blood
48	chr19:19411200-19423600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:19411200-19427400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:19411200-19427400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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