Variant report

Variant	rs73004959
Chromosome Location	chr19:19711139-19711140
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	chr19:19707335..19710149-chr19:19710538..19713142,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10500212	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12608729	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610185	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12610191	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996148	0.84[EUR][1000 genomes]
rs16996185	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17216525	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17216588	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17217098	0.87[EUR][1000 genomes]
rs3794991	0.86[AMR][1000 genomes]
rs57504626	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58847337	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004933	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004951	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73004962	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004966	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73004967	0.85[EUR][1000 genomes]
rs73004975	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19702400-19713200	Weak transcription	Brain Anterior Caudate	brain
2	chr19:19702600-19712400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:19702600-19713200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:19702600-19713400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:19702600-19713400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:19702600-19713600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:19702600-19719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19702800-19712400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:19703400-19717000	Weak transcription	Fetal Muscle Leg	muscle
10	chr19:19703800-19717000	Weak transcription	Spleen	Spleen
11	chr19:19704400-19712200	Weak transcription	Brain Germinal Matrix	brain
12	chr19:19706200-19712400	Weak transcription	Gastric	stomach
13	chr19:19706200-19712800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:19706400-19711800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:19706400-19712800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:19706400-19713000	Weak transcription	NHEK	skin
17	chr19:19706600-19712000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:19706600-19713200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:19706600-19713600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:19706600-19717000	Weak transcription	Esophagus	oesophagus
21	chr19:19706600-19728200	Weak transcription	Fetal Brain Male	brain
22	chr19:19707000-19712000	Weak transcription	Stomach Mucosa	stomach
23	chr19:19707000-19718600	Weak transcription	Fetal Lung	lung
24	chr19:19707200-19717000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr19:19707400-19712400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:19707400-19716800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:19707600-19716800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:19707600-19728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:19707800-19712600	Weak transcription	Placenta	Placenta
30	chr19:19707800-19714000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:19707800-19716800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:19708000-19716800	Enhancers	Fetal Thymus	thymus
33	chr19:19708800-19715000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:19708800-19716800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr19:19708800-19720000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:19708800-19724400	Weak transcription	NHDF-Ad	bronchial
37	chr19:19709000-19713600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19709000-19719200	Weak transcription	Fetal Brain Female	brain
39	chr19:19709200-19712400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:19709600-19712600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr19:19709600-19712800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr19:19710200-19711600	Weak transcription	Thymus	Thymus
43	chr19:19710200-19711800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:19710200-19712000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:19710200-19712600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:19710200-19713200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:19710200-19713200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr19:19710200-19714600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr19:19710200-19716800	Weak transcription	Dnd41	blood
50	chr19:19710200-19718800	Weak transcription	Fetal Stomach	stomach

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