Variant report

Variant	rs73402839
Chromosome Location	chr15:52409429-52409430
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	chr15:52385922..52387703-chr15:52408250..52411137,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs16953085	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7162885	0.96[AFR][1000 genomes]
rs7163133	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164357	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73402826	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402853	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402857	0.82[AFR][1000 genomes]
rs73402859	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402869	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402879	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035146	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52404800-52409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:52404800-52410600	Enhancers	Adipose Nuclei	Adipose
4	chr15:52404800-52416400	Weak transcription	Aorta	Aorta
5	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:52405000-52409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:52405000-52411800	Weak transcription	Ovary	ovary
8	chr15:52405000-52412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:52405000-52413200	Weak transcription	Primary T cells from cord blood	blood
10	chr15:52405000-52414800	Weak transcription	Primary B cells from cord blood	blood
11	chr15:52405000-52416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:52405000-52416400	Weak transcription	Gastric	stomach
13	chr15:52405000-52416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:52405000-52416600	Weak transcription	Esophagus	oesophagus
15	chr15:52405000-52420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
20	chr15:52405200-52412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:52405400-52426000	Weak transcription	Spleen	Spleen
22	chr15:52405600-52412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:52406000-52410200	Enhancers	Brain Germinal Matrix	brain
24	chr15:52406000-52412400	Weak transcription	Thymus	Thymus
25	chr15:52406000-52414200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr15:52406400-52427800	Weak transcription	Fetal Brain Male	brain
27	chr15:52406800-52409800	Enhancers	Liver	Liver
28	chr15:52406800-52410600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:52407000-52412200	Weak transcription	Fetal Brain Female	brain
30	chr15:52407200-52416400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:52407400-52409800	Enhancers	Fetal Intestine Large	intestine
32	chr15:52407400-52427600	Weak transcription	HSMMtube	muscle
33	chr15:52407600-52409800	Enhancers	Fetal Intestine Small	intestine
34	chr15:52407600-52417800	Weak transcription	Brain Anterior Caudate	brain
35	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
36	chr15:52407800-52409600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:52407800-52416800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:52407800-52428800	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
40	chr15:52408000-52416200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:52408000-52416600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr15:52408200-52416400	Weak transcription	NHDF-Ad	bronchial
43	chr15:52408200-52425800	Weak transcription	Small Intestine	intestine
44	chr15:52408400-52409600	Weak transcription	Pancreas	Pancrea
45	chr15:52408400-52409800	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:52408400-52414200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:52408600-52412000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:52408600-52416400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:52408600-52425600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:52408800-52410000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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