Variant report

Variant	rs58407864
Chromosome Location	chr9:103276155-103276156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TEX10-1	chr9:103275263-103276953	ucscGeneNc_uc004bbl_1

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12003523	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17741842	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17741914	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17741974	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17742650	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17814243	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17814768	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17814828	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17815616	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1930238	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1970632	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2417179	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34400489	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3983768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61001412	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7033848	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033969	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7041189	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7041892	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7042792	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73655579	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73655582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655584	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655586	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655588	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655590	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73657324	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7861317	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7862727	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7865385	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7866623	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58407864	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103255400-103277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
4	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
6	chr9:103260800-103287200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:103261200-103287600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
9	chr9:103263200-103312200	Weak transcription	Fetal Kidney	kidney
10	chr9:103263400-103278200	Weak transcription	Fetal Lung	lung
11	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
12	chr9:103264800-103277000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:103265200-103277800	Weak transcription	Ovary	ovary
14	chr9:103265400-103279800	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:103269400-103287000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:103270000-103289200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:103270200-103287200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:103270400-103283000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:103270600-103276600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:103270800-103290000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:103271600-103278000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:103272200-103279800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:103272600-103278000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:103272600-103307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:103272800-103283600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:103272800-103285400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:103273000-103285200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:103273000-103303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:103273200-103283800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:103273400-103282200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:103273400-103289400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:103273600-103279400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:103273600-103287200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
35	chr9:103273800-103283600	Weak transcription	Fetal Brain Female	brain
36	chr9:103273800-103287200	Weak transcription	Brain Germinal Matrix	brain
37	chr9:103274000-103278000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:103274200-103276400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:103274400-103289400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:103275600-103276600	Strong transcription	H1 Cell Line	embryonic stem cell

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