Variant report

Variant	rs73404813
Chromosome Location	chr15:52462697-52462698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52262525..52264741-chr15:52462329..52463854,2	MCF-7	breast:
2	chr15:52462256..52465166-chr15:52466100..52468864,2	MCF-7	breast:
3	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs12916135	0.82[AFR][1000 genomes]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964750	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs35712143	0.82[AFR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs4776010	0.84[AFR][1000 genomes]
rs4776013	0.84[AFR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs66566761	0.82[AFR][1000 genomes]
rs67725996	0.81[AFR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs7183278	0.84[AFR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:52439200-52463600	Weak transcription	NHEK	skin
4	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
8	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:52442600-52470400	Weak transcription	HMEC	breast
11	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:52445600-52463400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:52445600-52463600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
17	chr15:52447600-52463000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:52448800-52465200	Weak transcription	Liver	Liver
19	chr15:52452000-52463600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:52454200-52464000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:52454400-52463400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:52454400-52463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:52455800-52463000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:52455800-52463400	Weak transcription	Brain Angular Gyrus	brain
27	chr15:52455800-52463600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:52455800-52463600	Weak transcription	Primary B cells from cord blood	blood
29	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
30	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
31	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
32	chr15:52455800-52471000	Weak transcription	Gastric	stomach
33	chr15:52456000-52463000	Weak transcription	Fetal Thymus	thymus
34	chr15:52456000-52463400	Weak transcription	A549	lung
35	chr15:52456000-52464800	Weak transcription	Pancreas	Pancrea
36	chr15:52456000-52468400	Weak transcription	Ovary	ovary
37	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
41	chr15:52456200-52463000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:52456200-52463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:52456200-52463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:52456200-52463600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:52456200-52463600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:52456200-52467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:52456200-52468200	Weak transcription	Fetal Brain Female	brain
48	chr15:52456200-52468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach

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