Variant report

Variant	rs6477458
Chromosome Location	chr9:108498148-108498149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs41297177	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55982456	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056859	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59050784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59598160	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7026243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7026348	1.00[EUR][1000 genomes]
rs7027559	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73520072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522042	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867014	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[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	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108473200-108499800	Weak transcription	Gastric	stomach
2	chr9:108476400-108498200	Weak transcription	Left Ventricle	heart
3	chr9:108495400-108499400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
4	chr9:108495400-108500000	ZNF genes & repeats	Primary B cells from cord blood	blood
5	chr9:108495400-108500000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr9:108495400-108501400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:108495400-108501600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:108495600-108499000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr9:108496000-108498600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr9:108496400-108498400	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr9:108496400-108499200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:108496400-108500800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:108496600-108500400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:108497000-108499400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr9:108497000-108500000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr9:108497000-108500000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
17	chr9:108497000-108500400	ZNF genes & repeats	Brain Hippocampus Middle	brain
18	chr9:108497200-108498800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:108497200-108499400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:108497200-108500200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
21	chr9:108497600-108498200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:108497600-108498200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
23	chr9:108497600-108499400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
24	chr9:108497600-108499400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
25	chr9:108497600-108500600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr9:108497600-108501600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:108497600-108510800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:108497800-108498400	ZNF genes & repeats	Psoas Muscle	Psoas
29	chr9:108498000-108498400	ZNF genes & repeats	Ovary	ovary
30	chr9:108498000-108498600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:108498000-108511800	Weak transcription	K562	blood
32	chr9:108498000-108513200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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