Variant report

Variant	rs60299869
Chromosome Location	chr9:16443360-16443361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10511620	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10511621	0.92[EUR][1000 genomes]
rs16934644	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16934647	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16934660	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16934675	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16934679	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16934681	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927625	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3739715	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3814110	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41313973	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41313975	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57010092	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57310704	0.90[EUR][1000 genomes]
rs57937957	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58105894	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59049761	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60573475	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61159596	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61393085	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7021534	0.88[EUR][1000 genomes]
rs7041544	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7851973	0.92[EUR][1000 genomes]
rs7867445	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7871743	0.83[AMR][1000 genomes];0.88[EUR][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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv524954	chr9:16432544-16446091	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16421800-16460400	Weak transcription	Aorta	Aorta
2	chr9:16426200-16445200	Weak transcription	Adipose Nuclei	Adipose
3	chr9:16432600-16450600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:16434600-16445200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:16435000-16445400	Weak transcription	NH-A	brain
6	chr9:16435600-16444000	Weak transcription	Gastric	stomach
7	chr9:16437000-16445200	Weak transcription	Fetal Lung	lung
8	chr9:16437000-16445800	Weak transcription	HUVEC	blood vessel
9	chr9:16437400-16445200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:16437400-16445600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:16437400-16459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:16437600-16444400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:16437600-16445200	Weak transcription	NHLF	lung
14	chr9:16437600-16445400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:16437600-16450600	Weak transcription	Fetal Stomach	stomach
16	chr9:16437600-16450600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:16438600-16445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:16438800-16458800	Weak transcription	HSMM	muscle
19	chr9:16440400-16444600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:16441800-16443400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr9:16442000-16443400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr9:16442000-16443600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:16442000-16443800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:16442200-16443400	Enhancers	HMEC	breast
25	chr9:16442200-16443600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:16442400-16444200	Enhancers	Osteobl	bone
27	chr9:16442800-16444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:16442800-16445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:16442800-16445400	Enhancers	A549	lung
30	chr9:16442800-16445600	Weak transcription	NHEK	skin
31	chr9:16442800-16448200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:16442800-16453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:16442800-16455800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:16443000-16443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:16443000-16443800	Enhancers	Hela-S3	cervix
36	chr9:16443000-16445200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:16443000-16445200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:16443000-16445600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:16443000-16448400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:16443000-16449800	Weak transcription	Ovary	ovary
41	chr9:16443200-16443400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:16443200-16445200	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:16443200-16447800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:16443200-16448400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr9:16443200-16449400	Weak transcription	Placenta Amnion	Placenta Amnion

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