Variant report

Variant	rs17741974
Chromosome Location	chr9:103324710-103324711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103319527..103321211-chr9:103323263..103324822,2	K562	blood:

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

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

rs_ID	r²[population]
rs12003523	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17741842	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17741914	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17742650	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17814243	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17814768	1.00[CEU][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17814828	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17815616	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1930238	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1970632	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2417179	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34400489	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3983768	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58407864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61001412	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7033848	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7033969	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7041189	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7041892	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042792	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73655579	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73655582	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655584	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655586	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655588	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655590	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73657324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7861317	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7862727	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7865385	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7866623	0.89[AMR][1000 genomes];0.91[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
rs17741974	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
2	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
3	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
4	chr9:103278400-103333000	Weak transcription	Fetal Brain Male	brain
5	chr9:103300200-103327400	Weak transcription	Ovary	ovary
6	chr9:103307400-103331800	Weak transcription	Gastric	stomach
7	chr9:103307400-103332200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:103308000-103327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:103308000-103340200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:103311000-103328400	Weak transcription	Fetal Heart	heart
14	chr9:103311600-103330400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:103312000-103327200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:103312200-103328200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:103313200-103340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:103313400-103329400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:103313400-103331200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:103313400-103332000	Weak transcription	Fetal Lung	lung
22	chr9:103317200-103337400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:103318400-103326000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:103318400-103342400	Weak transcription	Brain Anterior Caudate	brain
25	chr9:103318600-103344000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:103319800-103326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:103319800-103336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:103320000-103327600	Weak transcription	HSMMtube	muscle
29	chr9:103320000-103336400	Weak transcription	HSMM	muscle
30	chr9:103320200-103331200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:103320600-103325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:103320600-103327600	Weak transcription	Fetal Brain Female	brain
33	chr9:103322400-103331600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr9:103322400-103340400	Weak transcription	Brain Substantia Nigra	brain
35	chr9:103322600-103331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:103322600-103341800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:103323000-103340200	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:103323200-103325000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:103323200-103325000	Strong transcription	Brain Germinal Matrix	brain
40	chr9:103323400-103332200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:103323400-103333400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:103323400-103342000	Weak transcription	Brain Angular Gyrus	brain
43	chr9:103323600-103324800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr9:103323600-103333000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:103323800-103340600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:103324000-103340200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:103324600-103325800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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