Variant report

Variant	rs2254373
Chromosome Location	chr9:8845315-8845316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1865341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865343	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2254372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570306	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570960	0.81[AFR][1000 genomes]
rs2570963	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814721	0.85[AFR][1000 genomes]
rs2814722	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr9:8835000-8850800	Weak transcription	Fetal Kidney	kidney
2	chr9:8835200-8852000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:8835200-8852400	Weak transcription	Aorta	Aorta
4	chr9:8835600-8850800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:8835600-8851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:8835800-8851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:8837400-8845400	Weak transcription	Ovary	ovary
8	chr9:8839600-8845600	Enhancers	Brain Hippocampus Middle	brain
9	chr9:8840600-8845600	Enhancers	Brain Substantia Nigra	brain
10	chr9:8843000-8845600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:8843000-8847000	Enhancers	Brain Cingulate Gyrus	brain
12	chr9:8843000-8852400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:8843000-8855200	Weak transcription	Fetal Stomach	stomach
14	chr9:8843000-8856600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:8843200-8846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:8843200-8854200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:8843400-8850800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:8843400-8850800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:8843600-8850800	Weak transcription	Fetal Lung	lung
20	chr9:8843800-8845400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:8843800-8850800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:8844000-8854400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:8844400-8845400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:8844600-8845400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:8844600-8848200	Enhancers	Brain Germinal Matrix	brain
26	chr9:8844800-8847000	Enhancers	Fetal Muscle Leg	muscle
27	chr9:8845000-8845800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:8845000-8846800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:8845000-8847000	Enhancers	Fetal Brain Female	brain
30	chr9:8845000-8847200	Enhancers	Fetal Brain Male	brain
31	chr9:8845200-8845400	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr9:8845200-8845400	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr9:8845200-8845400	Flanking Active TSS	Fetal Heart	heart
34	chr9:8845200-8845800	Enhancers	Psoas Muscle	Psoas
35	chr9:8845200-8846200	Enhancers	Cortex derived primary cultured neurospheres	brain

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