Variant report

Variant	rs13346052
Chromosome Location	chr19:39920897-39920898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39919482..39921784-chr19:39975995..39978521,2	K562	blood:
2	chr19:39915714..39918595-chr19:39919774..39922739,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105197	Chromatin interaction
ENSG00000269410	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10408589	1.00[EUR][1000 genomes]
rs10409917	1.00[EUR][1000 genomes]
rs10413140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413673	1.00[EUR][1000 genomes]
rs10415077	1.00[EUR][1000 genomes]
rs10415279	1.00[EUR][1000 genomes]
rs2230765	1.00[EUR][1000 genomes]
rs4100178	1.00[EUR][1000 genomes]
rs61569178	1.00[AMR][1000 genomes]
rs6508847	1.00[EUR][1000 genomes]
rs73547970	1.00[AMR][1000 genomes]
rs73547976	1.00[AMR][1000 genomes]
rs73547991	1.00[AMR][1000 genomes]
rs73547993	1.00[AMR][1000 genomes]
rs73547999	1.00[AMR][1000 genomes]
rs73549905	1.00[AMR][1000 genomes]
rs73549906	1.00[AMR][1000 genomes]
rs73549912	1.00[AMR][1000 genomes]
rs73549922	1.00[AMR][1000 genomes]
rs73549928	1.00[AMR][1000 genomes]
rs73549930	1.00[AMR][1000 genomes]
rs73549931	1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	1.00[AMR][1000 genomes]
rs73551839	1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
7	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39921000	Weak transcription	Small Intestine	intestine
2	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39905000-39921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39905400-39921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:39905400-39921200	Weak transcription	K562	blood
6	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39905600-39921600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
9	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39906400-39921200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:39910000-39921000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:39910000-39921200	Weak transcription	NHEK	skin
13	chr19:39910000-39922600	Weak transcription	Liver	Liver
14	chr19:39911400-39923400	Weak transcription	Fetal Brain Male	brain
15	chr19:39913600-39921400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:39913800-39922800	Weak transcription	Psoas Muscle	Psoas
17	chr19:39914000-39921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:39914000-39921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:39914800-39921600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:39915200-39921600	Weak transcription	Primary B cells from cord blood	blood
21	chr19:39915200-39921600	Weak transcription	Esophagus	oesophagus
22	chr19:39915400-39921000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr19:39915400-39921200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:39915400-39921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:39915400-39921400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr19:39915400-39923000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:39915600-39921200	Weak transcription	GM12878-XiMat	blood
28	chr19:39915600-39921600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr19:39915600-39921600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:39915600-39921600	Weak transcription	Gastric	stomach
31	chr19:39915800-39921600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:39916000-39921000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:39916200-39921800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:39916800-39921200	Weak transcription	Brain Germinal Matrix	brain
35	chr19:39916800-39923000	Weak transcription	Dnd41	blood
36	chr19:39917000-39921600	Weak transcription	Thymus	Thymus
37	chr19:39917200-39921800	Weak transcription	Primary T cells from cord blood	blood
38	chr19:39917400-39921200	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:39917400-39921800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:39917400-39922800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:39917400-39923000	Weak transcription	Brain Angular Gyrus	brain
42	chr19:39917400-39923000	Weak transcription	Brain Substantia Nigra	brain
43	chr19:39918000-39921600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:39918000-39922200	Enhancers	Placenta	Placenta
45	chr19:39919600-39921000	Weak transcription	Stomach Mucosa	stomach
46	chr19:39919600-39921200	Weak transcription	Spleen	Spleen
47	chr19:39919600-39921400	Weak transcription	Fetal Brain Female	brain
48	chr19:39919600-39921400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr19:39919600-39921600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:39919600-39921600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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