Variant report

Variant	rs650424
Chromosome Location	chr15:40089819-40089820
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	chr15:40081008..40084255-chr15:40089544..40091959,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11636194	1.00[AMR][1000 genomes]
rs166704	1.00[AMR][1000 genomes]
rs16952166	1.00[AMR][1000 genomes]
rs16969385	1.00[AMR][1000 genomes]
rs16969567	1.00[AMR][1000 genomes]
rs16969594	1.00[AMR][1000 genomes]
rs16969623	1.00[AMR][1000 genomes]
rs16969673	1.00[AMR][1000 genomes]
rs16969697	1.00[AMR][1000 genomes]
rs16969698	1.00[AMR][1000 genomes]
rs16969766	1.00[AMR][1000 genomes]
rs16969787	1.00[AMR][1000 genomes]
rs16969794	1.00[AMR][1000 genomes]
rs16969798	1.00[AMR][1000 genomes]
rs16969817	1.00[AMR][1000 genomes]
rs175728	1.00[AMR][1000 genomes]
rs2631699	1.00[AMR][1000 genomes]
rs2640643	1.00[AMR][1000 genomes]
rs275722	1.00[AMR][1000 genomes]
rs275735	1.00[AMR][1000 genomes]
rs275740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs275741	1.00[AMR][1000 genomes]
rs275743	1.00[AMR][1000 genomes]
rs275745	1.00[AMR][1000 genomes]
rs423983	1.00[AMR][1000 genomes]
rs56932964	1.00[AMR][1000 genomes]
rs573879	1.00[AMR][1000 genomes]
rs58368477	1.00[AMR][1000 genomes]
rs584244	1.00[AMR][1000 genomes]
rs60403575	1.00[AMR][1000 genomes]
rs60701446	1.00[AMR][1000 genomes]
rs649015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs684438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73391276	1.00[AMR][1000 genomes]
rs73391292	1.00[AMR][1000 genomes]
rs73391299	1.00[AMR][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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
2	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:40077200-40092600	Weak transcription	NHEK	skin
5	chr15:40077200-40093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:40080000-40095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:40080400-40095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40081000-40092400	Weak transcription	HSMMtube	muscle
10	chr15:40081200-40090400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:40081200-40092200	Weak transcription	NH-A	brain
12	chr15:40081200-40093400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:40081400-40092800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:40081400-40100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:40082400-40090400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:40082600-40091800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:40082600-40092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40084800-40090600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:40085400-40090400	Weak transcription	Adipose Nuclei	Adipose
20	chr15:40085400-40091600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:40085400-40092200	Weak transcription	NHDF-Ad	bronchial
22	chr15:40086000-40090200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:40086000-40090400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:40086000-40095600	Weak transcription	HUVEC	blood vessel
25	chr15:40086400-40090400	Weak transcription	NHLF	lung
26	chr15:40086400-40093600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:40087800-40090200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:40088000-40095000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:40088800-40090600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr15:40088800-40091800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:40088800-40094600	Strong transcription	Osteobl	bone
32	chr15:40089600-40090000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:40089600-40090000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr15:40089600-40090000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:40089600-40094400	Strong transcription	Aorta	Aorta
36	chr15:40089600-40094400	Strong transcription	HSMM	muscle
37	chr15:40089600-40099400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:40089800-40094400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:40089800-40094400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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