Variant report

Variant	rs56002461
Chromosome Location	chr9:98578637-98578638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98563811..98565847-chr9:98577723..98580063,2	MCF-7	breast:
2	chr9:98578285..98580022-chr9:98583507..98586457,2	MCF-7	breast:
3	chr9:98571684..98573454-chr9:98577064..98579753,2	MCF-7	breast:
4	chr9:98577023..98579790-chr9:98637878..98639433,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs55747426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656566	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656583	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859542	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7874318	0.89[AFR][1000 genomes];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	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:40 , 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	chr9:98570600-98579200	Weak transcription	Liver	Liver
8	chr9:98570600-98579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:98571000-98582000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:98572400-98579000	Weak transcription	Primary T cells from cord blood	blood
13	chr9:98572800-98582400	Weak transcription	Brain Germinal Matrix	brain
14	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
15	chr9:98575800-98579600	Enhancers	HSMM	muscle
16	chr9:98575800-98579800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:98576000-98579200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:98576000-98579800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:98576000-98579800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:98576000-98580000	Enhancers	A549	lung
21	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
22	chr9:98576600-98581600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:98576800-98582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:98576800-98584800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:98577600-98578800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:98577600-98579200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:98577600-98585600	Weak transcription	Pancreas	Pancrea
28	chr9:98577800-98578800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr9:98577800-98579000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr9:98577800-98579000	Weak transcription	Ovary	ovary
31	chr9:98577800-98579000	Weak transcription	HUVEC	blood vessel
32	chr9:98577800-98584400	Weak transcription	NHLF	lung
33	chr9:98578000-98578800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr9:98578000-98578800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:98578200-98578800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr9:98578200-98579800	Enhancers	Hela-S3	cervix
37	chr9:98578400-98578800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:98578400-98579200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:98578600-98580800	Weak transcription	Fetal Stomach	stomach
40	chr9:98578600-98581800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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