Variant report

Variant	rs28551602
Chromosome Location	chr19:40857621-40857622
allele	A/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	POLR2A	chr19:40857304-40857861	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40854558..40856307-chr19:40856338..40858284,2	MCF-7	breast:

Variant related genes	Relation type
C19orf47	TF binding region
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10414606	1.00[AMR][1000 genomes]
rs10417028	0.82[AFR][1000 genomes]
rs10417233	1.00[AMR][1000 genomes]
rs10421448	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424704	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40855400-40859200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:40855400-40864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:40855600-40857800	Weak transcription	Fetal Stomach	stomach
4	chr19:40855600-40859200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr19:40855600-40859800	Weak transcription	Fetal Intestine Small	intestine
6	chr19:40855600-40861400	Weak transcription	Stomach Mucosa	stomach
7	chr19:40855600-40861600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:40855600-40861600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr19:40855600-40861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:40855600-40861600	Weak transcription	GM12878-XiMat	blood
11	chr19:40855600-40861800	Weak transcription	Primary T cells from cord blood	blood
12	chr19:40855600-40861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:40855600-40861800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:40855600-40861800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:40855600-40861800	Weak transcription	Brain Germinal Matrix	brain
16	chr19:40855600-40861800	Weak transcription	Ovary	ovary
17	chr19:40855600-40861800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:40855600-40861800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr19:40855600-40862200	Weak transcription	Adipose Nuclei	Adipose
20	chr19:40855600-40862600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr19:40855600-40862800	Weak transcription	Brain Anterior Caudate	brain
22	chr19:40855600-40862800	Weak transcription	Fetal Lung	lung
23	chr19:40855600-40863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:40855600-40863200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:40855600-40863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:40855600-40863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:40855600-40863600	Weak transcription	Fetal Brain Female	brain
28	chr19:40855600-40863800	Weak transcription	Liver	Liver
29	chr19:40855600-40864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:40855600-40864000	Weak transcription	Spleen	Spleen
31	chr19:40855600-40864000	Weak transcription	NH-A	brain
32	chr19:40855600-40864400	Weak transcription	Placenta	Placenta
33	chr19:40855600-40865200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:40855600-40865200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:40855600-40865200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:40855600-40865200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:40855600-40865200	Weak transcription	Thymus	Thymus
38	chr19:40855600-40865200	Weak transcription	A549	lung
39	chr19:40855600-40865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:40855600-40865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:40855600-40865400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:40855600-40865800	Weak transcription	K562	blood
43	chr19:40855600-40866000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:40855600-40866200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:40855600-40866200	Weak transcription	Esophagus	oesophagus
46	chr19:40855600-40866600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:40855600-40868800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:40855600-40868800	Weak transcription	HSMM	muscle
49	chr19:40855600-40869000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr19:40855600-40869000	Weak transcription	Osteobl	bone

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