Variant report

Variant	rs28714112
Chromosome Location	chr19:40304940-40304941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40301803..40305513-chr19:40314560..40316955,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10403751	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410397	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412290	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414733	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414955	1.00[EUR][1000 genomes]
rs10416176	1.00[EUR][1000 genomes]
rs11883291	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56387916	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58565953	1.00[EUR][1000 genomes]
rs59903001	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59946095	1.00[EUR][1000 genomes]
rs60983054	1.00[EUR][1000 genomes]
rs73543039	1.00[EUR][1000 genomes]
rs73543045	1.00[EUR][1000 genomes]
rs73930604	1.00[EUR][1000 genomes]
rs73930650	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930653	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930657	1.00[EUR][1000 genomes]
rs73930778	1.00[EUR][1000 genomes]
rs73930779	1.00[EUR][1000 genomes]
rs73930780	1.00[EUR][1000 genomes]
rs8100743	1.00[EUR][1000 genomes]
rs8101720	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40296200-40314200	Weak transcription	Right Ventricle	heart
2	chr19:40298800-40314200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:40299800-40313600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:40300200-40314200	Weak transcription	Gastric	stomach
5	chr19:40300600-40306800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:40300800-40306600	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:40300800-40313400	Weak transcription	Pancreas	Pancrea
8	chr19:40301400-40308800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:40301400-40309400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:40301600-40306400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:40301600-40314200	Weak transcription	Ovary	ovary
12	chr19:40301600-40314400	Weak transcription	Primary B cells from cord blood	blood
13	chr19:40301600-40314400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr19:40301800-40306600	Weak transcription	A549	lung
15	chr19:40302000-40305600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40302600-40306800	Weak transcription	Lung	lung
17	chr19:40302600-40314400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:40302800-40314200	Weak transcription	Brain Angular Gyrus	brain
19	chr19:40303000-40314200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:40303000-40314200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:40303200-40314200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr19:40303600-40306400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:40303600-40306600	Weak transcription	Left Ventricle	heart
24	chr19:40303600-40306800	Weak transcription	Fetal Stomach	stomach
25	chr19:40303800-40306600	Weak transcription	Fetal Brain Female	brain
26	chr19:40303800-40306800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:40303800-40314200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:40304000-40306800	Weak transcription	Psoas Muscle	Psoas
29	chr19:40304000-40313400	Weak transcription	Brain Germinal Matrix	brain
30	chr19:40304000-40314200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:40304200-40306600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:40304200-40308800	Weak transcription	Spleen	Spleen
33	chr19:40304400-40306800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr19:40304600-40305200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:40304600-40306800	Weak transcription	Aorta	Aorta
36	chr19:40304600-40307000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr19:40304600-40308000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr19:40304600-40314200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:40304600-40314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:40304600-40314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:40304800-40305400	Weak transcription	Primary T cells from cord blood	blood
42	chr19:40304800-40306600	Weak transcription	Fetal Muscle Leg	muscle
43	chr19:40304800-40306800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:40304800-40306800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:40304800-40306800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:40304800-40306800	Weak transcription	Fetal Muscle Trunk	muscle

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