Variant report

Variant	rs17813447
Chromosome Location	chr9:103173925-103173926
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213031065..213031850-chr9:103173442..103174223,2	Hela-S3	cervix:
2	chr9:103162892..103165922-chr9:103171980..103175521,3	MCF-7	breast:
3	chr9:103171653..103179256-chr9:103186952..103193020,13	MCF-7	breast:
4	chr9:103169579..103171733-chr9:103173238..103174816,2	K562	blood:
5	chr12:49715778..49716730-chr9:103173422..103174116,2	NB4	blood:
6	chr9:103114138..103117790-chr9:103172786..103175922,6	MCF-7	breast:
7	chr9:103114959..103115741-chr9:103173676..103174182,2	MCF-7	breast:
8	chr9:103172431..103174027-chr9:103177638..103179534,2	MCF-7	breast:
9	chr9:103169516..103171661-chr9:103172507..103175663,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000136891	Chromatin interaction
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1016176	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1016177	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17740576	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17741914	1.00[YRI][hapmap]
rs17813663	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17813801	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs17813854	0.85[EUR][1000 genomes]
rs17815616	1.00[YRI][hapmap]
rs2026998	0.89[EUR][1000 genomes]
rs2151107	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35438121	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41274963	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4395949	0.89[EUR][1000 genomes]
rs56179916	0.91[EUR][1000 genomes]
rs56313595	0.88[EUR][1000 genomes]
rs56720423	0.85[EUR][1000 genomes]
rs57241635	0.88[EUR][1000 genomes]
rs58030694	0.88[EUR][1000 genomes]
rs58698990	0.85[EUR][1000 genomes]
rs59668196	0.83[EUR][1000 genomes]
rs61306839	0.87[EUR][1000 genomes]
rs61386923	0.88[EUR][1000 genomes]
rs72733393	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72733395	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72733397	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655529	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73655530	0.89[EUR][1000 genomes]
rs73655531	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73655532	0.89[EUR][1000 genomes]
rs73655533	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73655534	0.89[EUR][1000 genomes]
rs73655535	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73655536	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73655537	0.89[EUR][1000 genomes]
rs73655539	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655540	0.88[EUR][1000 genomes]
rs73655541	0.88[EUR][1000 genomes]
rs73655542	0.88[EUR][1000 genomes]
rs73655543	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655544	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655545	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655546	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655547	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73655549	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73655550	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73655551	0.85[EUR][1000 genomes]
rs73655553	0.85[EUR][1000 genomes]
rs73655554	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17813447	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103172400-103174600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr9:103173200-103174800	Active TSS	Rectal Smooth Muscle	rectum
3	chr9:103173400-103174000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:103173400-103174000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr9:103173400-103174200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:103173400-103174400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:103173400-103174400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:103173400-103174400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:103173400-103174400	Active TSS	Fetal Kidney	kidney
10	chr9:103173400-103174600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:103173400-103174600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr9:103173400-103174600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr9:103173400-103174600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr9:103173400-103174600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr9:103173400-103174600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:103173400-103174600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:103173400-103174600	Active TSS	Colonic Mucosa	Colon
18	chr9:103173400-103174600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr9:103173400-103174600	Active TSS	GM12878-XiMat	blood
20	chr9:103173400-103174600	Flanking Active TSS	NHEK	skin
21	chr9:103173400-103174800	Active TSS	Brain Angular Gyrus	brain
22	chr9:103173400-103174800	Active TSS	Brain Substantia Nigra	brain
23	chr9:103173600-103174000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr9:103173600-103174000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:103173600-103174000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:103173600-103174000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:103173600-103174000	Flanking Active TSS	NHLF	lung
28	chr9:103173600-103174000	Flanking Active TSS	Osteobl	bone
29	chr9:103173600-103174200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:103173600-103174200	Active TSS	Fetal Brain Male	brain
31	chr9:103173600-103174200	Active TSS	Lung	lung
32	chr9:103173600-103174200	Active TSS	NH-A	brain
33	chr9:103173600-103174400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr9:103173600-103174400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:103173600-103174400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:103173600-103174400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr9:103173600-103174400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:103173600-103174400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr9:103173600-103174400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr9:103173600-103174400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr9:103173600-103174400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:103173600-103174400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:103173600-103174400	Active TSS	Brain Anterior Caudate	brain
44	chr9:103173600-103174400	Flanking Active TSS	Placenta	Placenta
45	chr9:103173600-103174400	Active TSS	Placenta Amnion	Placenta Amnion
46	chr9:103173600-103174400	Active TSS	Thymus	Thymus
47	chr9:103173600-103174600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:103173600-103174600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:103173600-103174600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr9:103173600-103174600	Active TSS	HUES6 Cell Line	embryonic stem cell

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