Variant report

Variant	rs17813854
Chromosome Location	chr9:103221300-103221301
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	chr9:103218360..103221839-chr9:103223201..103225768,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf30-3	chr9:103221120-103224907	ncRnaDb_ncrna_FR405056_1

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1016176	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1016177	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12237166	0.84[EUR][1000 genomes]
rs17740576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17741842	0.82[ASW][hapmap];0.94[GIH][hapmap]
rs17813447	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs17813663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17813801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17814768	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs17814828	0.94[GIH][hapmap]
rs2026998	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2151107	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2417179	0.83[AMR][1000 genomes]
rs35438121	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41274963	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4395949	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56179916	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56313595	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56720423	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57241635	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58030694	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58698990	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59668196	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61306839	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61386923	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7034154	0.82[EUR][1000 genomes]
rs7041189	0.94[GIH][hapmap]
rs7041933	0.82[EUR][1000 genomes]
rs7046659	0.80[EUR][1000 genomes]
rs72733393	0.84[EUR][1000 genomes]
rs72733395	0.84[EUR][1000 genomes]
rs72733397	0.84[EUR][1000 genomes]
rs73655529	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73655530	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655531	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655532	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655533	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655534	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655535	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655536	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655537	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655539	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655540	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655541	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655542	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655543	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655544	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655545	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655546	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655547	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73655549	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655550	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655579	0.81[AMR][1000 genomes]
rs7865385	0.94[GIH][hapmap]
rs7866623	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17813854	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
4	chr9:103207000-103227400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:103208800-103227200	Weak transcription	Brain Angular Gyrus	brain
6	chr9:103208800-103227800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:103209600-103227400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:103214200-103224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:103214600-103221600	Weak transcription	Lung	lung
10	chr9:103214600-103222600	Weak transcription	Thymus	Thymus
11	chr9:103214600-103224800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:103215000-103222800	Weak transcription	Fetal Stomach	stomach
13	chr9:103215200-103221400	Weak transcription	Esophagus	oesophagus
14	chr9:103215200-103224600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:103215600-103221800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:103215600-103227400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:103215600-103231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:103215800-103224600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:103215800-103227400	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:103216000-103221600	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:103216200-103224600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:103216200-103225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:103216600-103223800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:103216600-103223800	Weak transcription	NH-A	brain
25	chr9:103216600-103224600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:103216600-103228400	Weak transcription	Adipose Nuclei	Adipose
27	chr9:103216600-103235000	Weak transcription	Aorta	Aorta
28	chr9:103216800-103221800	Weak transcription	HSMMtube	muscle
29	chr9:103216800-103222600	Weak transcription	Primary T cells from cord blood	blood
30	chr9:103216800-103223000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:103216800-103224800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:103216800-103225600	Weak transcription	A549	lung
33	chr9:103216800-103227400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:103216800-103227600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:103216800-103227600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:103216800-103228600	Weak transcription	Left Ventricle	heart
37	chr9:103216800-103228600	Weak transcription	Pancreas	Pancrea
38	chr9:103216800-103235000	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:103217000-103234800	Weak transcription	Fetal Brain Female	brain
40	chr9:103217200-103234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:103217400-103222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:103217400-103223600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:103217400-103227600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:103218200-103227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:103218200-103235000	Weak transcription	NHLF	lung
46	chr9:103218400-103221400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:103218400-103222800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:103218400-103222800	Weak transcription	Ovary	ovary
49	chr9:103218400-103235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:103218800-103222000	Weak transcription	NHDF-Ad	bronchial

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