Variant report

Variant	rs7033848
Chromosome Location	chr9:103262661-103262662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12003523	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12004257	0.80[EUR][1000 genomes]
rs17741842	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17741914	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17741974	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17742650	0.86[AMR][1000 genomes]
rs17814243	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17814768	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17814828	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17815616	0.86[AMR][1000 genomes]
rs1930238	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1970632	0.86[AMR][1000 genomes]
rs2026998	1.00[YRI][hapmap]
rs2417179	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34400489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3983768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4395949	1.00[YRI][hapmap]
rs58407864	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61001412	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7033969	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041189	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041892	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042792	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655579	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655582	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73655584	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73655586	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73655588	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73655590	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73657324	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7861317	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862727	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7865385	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866623	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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
rs7033848	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103238200-103264200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:103238200-103274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:103255200-103271000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:103255400-103277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:103255600-103265800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:103255600-103266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:103255600-103272400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:103255600-103272400	Weak transcription	Fetal Brain Female	brain
9	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:103255800-103266000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:103255800-103272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:103256200-103265000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
14	chr9:103256400-103271600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:103257000-103272400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:103258200-103263600	Weak transcription	Brain Germinal Matrix	brain
18	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
19	chr9:103260400-103264800	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:103260400-103272200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:103260400-103272200	Weak transcription	Brain Substantia Nigra	brain
22	chr9:103260800-103262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:103260800-103287200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:103261000-103262800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:103261000-103263800	Weak transcription	Brain Angular Gyrus	brain
26	chr9:103261000-103265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:103261000-103272400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:103261200-103264000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:103261200-103267200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:103261200-103287600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:103261600-103263000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
33	chr9:103262600-103263000	Weak transcription	Fetal Lung	lung
34	chr9:103262600-103272400	Weak transcription	Fetal Muscle Leg	muscle

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