Variant report

Variant	rs1004489
Chromosome Location	chr9:8733398-8733399
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10977261	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4740958	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs4742529	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7854391	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs7872708	0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv6474	chr9:8706602-8751414	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8710600-8733600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:8718400-8733600	Weak transcription	Psoas Muscle	Psoas
3	chr9:8722000-8744600	Weak transcription	Dnd41	blood
4	chr9:8724800-8733400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:8725000-8733600	Weak transcription	Ovary	ovary
6	chr9:8727000-8733600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:8727800-8733400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:8730800-8733400	Enhancers	Brain Cingulate Gyrus	brain
9	chr9:8731200-8733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:8731200-8733600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:8731400-8733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:8731800-8733400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr9:8731800-8733400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:8731800-8733400	Enhancers	Brain Anterior Caudate	brain
15	chr9:8731800-8735000	Enhancers	Fetal Lung	lung
16	chr9:8732200-8735400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:8732400-8733400	Enhancers	Brain Substantia Nigra	brain
18	chr9:8732400-8733800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr9:8732600-8733600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:8732600-8735600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr9:8732800-8733400	Enhancers	Fetal Muscle Leg	muscle
22	chr9:8732800-8733600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:8732800-8733600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr9:8732800-8733600	Enhancers	Fetal Kidney	kidney
25	chr9:8732800-8734000	Enhancers	HSMM	muscle
26	chr9:8732800-8734600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:8732800-8735000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:8732800-8735600	Enhancers	Fetal Brain Male	brain
29	chr9:8733000-8733400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:8733000-8733400	Enhancers	HUVEC	blood vessel
31	chr9:8733000-8733600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:8733000-8733800	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:8733000-8737200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:8733200-8733400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr9:8733200-8733400	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr9:8733200-8733400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:8733200-8733600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:8733200-8733600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:8733200-8733600	Flanking Active TSS	Fetal Brain Female	brain
40	chr9:8733200-8733600	Enhancers	Fetal Stomach	stomach
41	chr9:8733200-8733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:8733200-8733800	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr9:8733200-8734000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:8733200-8734200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:8733200-8734400	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr9:8733200-8734600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr9:8733200-8734800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:8733200-8735200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:8733200-8735200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:8733200-8736200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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