Variant report

Variant	rs12004258
Chromosome Location	chr9:98580655-98580656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3991704	0.89[AFR][1000 genomes]
rs4742769	0.85[AFR][1000 genomes]
rs55870020	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs56275194	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs58715455	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59046245	0.90[AFR][1000 genomes]
rs59510923	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs60301271	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6478983	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7021641	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7030427	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7031397	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7046189	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7047126	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73656542	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73656543	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73656554	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73656561	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73656564	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7860019	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs892647	0.93[AFR][1000 genomes];0.90[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570400-98580800	Weak transcription	Fetal Intestine Small	intestine
2	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
4	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
5	chr9:98570400-98593200	Weak transcription	Gastric	stomach
6	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
7	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:98571000-98582000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:98572800-98582400	Weak transcription	Brain Germinal Matrix	brain
11	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
12	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
13	chr9:98576600-98581600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:98576800-98582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:98576800-98584800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:98577600-98585600	Weak transcription	Pancreas	Pancrea
17	chr9:98577800-98584400	Weak transcription	NHLF	lung
18	chr9:98578600-98580800	Weak transcription	Fetal Stomach	stomach
19	chr9:98578600-98581800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:98578800-98581200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:98578800-98581400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:98578800-98581600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:98579000-98581000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:98579000-98582000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:98579200-98580800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:98579200-98582200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:98579200-98584400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:98579600-98580800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:98579600-98581200	Weak transcription	HUVEC	blood vessel
30	chr9:98579800-98581200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:98579800-98581400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98579800-98583600	Weak transcription	Ovary	ovary
33	chr9:98579800-98583800	Weak transcription	Hela-S3	cervix
34	chr9:98580000-98582600	Weak transcription	Liver	Liver
35	chr9:98580000-98584600	Weak transcription	A549	lung

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