Variant report

Variant	rs390529
Chromosome Location	chr9:108006948-108006949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:107948857..107951560-chr9:108005097..108008240,3	MCF-7	breast:
2	chr9:108005738..108008360-chr9:108117762..108120177,2	MCF-7	breast:
3	chr9:107687369..107691649-chr9:108006197..108009884,7	MCF-7	breast:
4	chr9:108006932..108009449-chr9:108036462..108038843,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FSD1L-3	chr9:108006929-108007185	NONHSAT133813

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction
ENSG00000238208	Chromatin interaction
ENSG00000226334	Chromatin interaction
ENSG00000165029	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs167867	0.85[AMR][1000 genomes]
rs1705491	0.81[AMR][1000 genomes]
rs170582	0.83[AMR][1000 genomes]
rs2441214	0.81[AMR][1000 genomes]
rs327960	0.83[AMR][1000 genomes]
rs327966	0.83[AMR][1000 genomes]
rs380104	0.81[AMR][1000 genomes]
rs383272	0.81[AMR][1000 genomes]
rs388679	0.81[AMR][1000 genomes]
rs398454	0.81[AMR][1000 genomes]
rs419443	0.81[AMR][1000 genomes]
rs435379	0.81[AMR][1000 genomes]
rs439308	0.81[AMR][1000 genomes]
rs446641	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893691	chr9:107994629-108020284	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3368118	chr9:108006181-108008254	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108004800-108009400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr9:108005000-108009200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:108006000-108008000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:108006000-108008400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr9:108006000-108008600	Active TSS	A549	lung
6	chr9:108006200-108007200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:108006200-108007400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108006200-108007400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
9	chr9:108006200-108007600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:108006200-108007600	Active TSS	Fetal Muscle Leg	muscle
11	chr9:108006200-108007800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:108006200-108007800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:108006200-108008000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:108006200-108008000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:108006200-108008200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr9:108006200-108008200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:108006200-108008200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:108006200-108008200	Active TSS	Colon Smooth Muscle	Colon
19	chr9:108006200-108008200	Active TSS	Esophagus	oesophagus
20	chr9:108006200-108008200	Active TSS	Placenta Amnion	Placenta Amnion
21	chr9:108006200-108008200	Active TSS	HSMMtube	muscle
22	chr9:108006200-108008400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:108006200-108008400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:108006200-108008400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:108006200-108008400	Active TSS	Left Ventricle	heart
26	chr9:108006200-108008400	Active TSS	Stomach Smooth Muscle	stomach
27	chr9:108006200-108008600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:108006200-108008600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr9:108006200-108008600	Active TSS	Ovary	ovary
30	chr9:108006200-108008600	Active TSS	Psoas Muscle	Psoas
31	chr9:108006200-108009000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr9:108006200-108009000	Active TSS	Aorta	Aorta
33	chr9:108006200-108009000	Active TSS	Brain Germinal Matrix	brain
34	chr9:108006200-108009000	Active TSS	Duodenum Mucosa	Duodenum
35	chr9:108006200-108009200	Active TSS	Right Atrium	heart
36	chr9:108006200-108009600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:108006200-108010000	Active TSS	Brain Cingulate Gyrus	brain
38	chr9:108006200-108010400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:108006200-108011800	Active TSS	Brain Hippocampus Middle	brain
40	chr9:108006400-108007200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:108006400-108007400	Active TSS	Fetal Stomach	stomach
42	chr9:108006400-108007800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr9:108006400-108007800	Active TSS	HSMM	muscle
44	chr9:108006400-108008000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr9:108006400-108008000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr9:108006400-108008000	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:108006400-108008000	Active TSS	NHLF	lung
48	chr9:108006400-108008200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:108006400-108008200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:108006400-108008200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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