Variant report

Variant	rs28398252
Chromosome Location	chr9:104074398-104074399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:103988903..103989790-chr9:104073704..104074549,2	K562	blood:
2	chr9:103462912..103463800-chr9:104073433..104074690,5	K562	blood:
3	chr9:104022273..104023207-chr9:104074087..104074825,2	MCF-7	breast:
4	chr9:103364235..103365012-chr9:104074061..104074764,2	MCF-7	breast:
5	chr9:103476522..103477341-chr9:104073801..104074438,2	MCF-7	breast:
6	chr9:103362677..103364065-chr9:104073640..104074719,9	MCF-7	breast:
7	chr9:103363137..103364168-chr9:104073197..104074607,7	K562	blood:
8	chr9:103881309..103882121-chr9:104073642..104074623,5	MCF-7	breast:
9	chr9:103364305..103365019-chr9:104073743..104074587,4	MCF-7	breast:
10	chr9:103363061..103364025-chr9:104073627..104074488,4	MCF-7	breast:
11	chr9:103881294..103882107-chr9:104073696..104074727,3	MCF-7	breast:
12	chr9:103364791..103365296-chr9:104073724..104074625,2	K562	blood:
13	chr9:104069628..104072510-chr9:104073819..104075636,2	MCF-7	breast:
14	chr9:103881236..103882233-chr9:104073706..104074558,3	K562	blood:

No data

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10118704	0.80[AMR][1000 genomes]
rs10120191	0.84[EUR][1000 genomes]
rs10124153	0.80[AMR][1000 genomes]
rs10217289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217724	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12337610	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338304	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12352498	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341768	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13440036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13440141	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13440426	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28489693	1.00[ASN][1000 genomes]
rs55805275	1.00[ASN][1000 genomes]
rs56198539	1.00[ASN][1000 genomes]
rs6479047	0.95[EUR][1000 genomes]
rs6479048	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028337	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855910	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037157	chr9:104045761-104149233	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1049740	chr9:104049624-104075825	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104069400-104075000	Weak transcription	Fetal Brain Male	brain
2	chr9:104069600-104074800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:104069800-104075000	Weak transcription	Brain Germinal Matrix	brain
4	chr9:104069800-104075000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:104070800-104075000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:104072400-104075800	Enhancers	Brain Hippocampus Middle	brain
7	chr9:104073000-104088600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:104073600-104075200	Enhancers	Brain Angular Gyrus	brain
9	chr9:104073800-104075200	Enhancers	HSMM	muscle
10	chr9:104073800-104082600	Weak transcription	Brain Anterior Caudate	brain
11	chr9:104074200-104074400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr9:104074200-104074400	Enhancers	Brain Substantia Nigra	brain
13	chr9:104074200-104074400	Enhancers	K562	blood
14	chr9:104074200-104074600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr9:104074200-104074600	Enhancers	Adipose Nuclei	Adipose
16	chr9:104074200-104074600	Enhancers	A549	lung
17	chr9:104074200-104075200	Enhancers	HepG2	liver
18	chr9:104074200-104075400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:104074200-104075400	Enhancers	Fetal Lung	lung
20	chr9:104074200-104075400	Enhancers	HSMMtube	muscle
21	chr9:104074200-104080800	Enhancers	Liver	Liver

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