Variant report

Variant	rs13291670
Chromosome Location	chr9:103361572-103361573
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103360698..103363075-chr9:104159012..104161996,2	MCF-7	breast:
2	chr9:103279571..103281078-chr9:103358915..103361806,2	K562	blood:
3	chr9:103358110..103359783-chr9:103360702..103363224,2	MCF-7	breast:
4	chr9:103361504..103363020-chr9:103366654..103368893,2	K562	blood:
5	chr9:103350659..103353280-chr9:103360412..103361939,2	K562	blood:
6	chr9:103278757..103281071-chr9:103359482..103361806,2	K562	blood:

Variant related genes	Relation type
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10989168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1135455	0.93[ASN][1000 genomes]
rs1226588	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1226592	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1226594	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1226596	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13301089	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1760290	0.92[ASN][1000 genomes]
rs2151597	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2489363	0.93[ASN][1000 genomes]
rs2489364	0.92[ASN][1000 genomes]
rs2780958	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2780959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2800288	0.95[ASN][1000 genomes]
rs72735191	0.97[ASN][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	nsv893624	chr9:103351931-103416553	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13291670	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103360200-103361800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:103360600-103361600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr9:103360600-103361600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:103360600-103361600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr9:103360600-103361600	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr9:103360600-103361800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:103360600-103361800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:103360600-103361800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr9:103360600-103361800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:103360600-103361800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr9:103360600-103361800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:103360600-103361800	Active TSS	A549	lung
13	chr9:103360600-103361800	Flanking Active TSS	HUVEC	blood vessel
14	chr9:103360600-103361800	Active TSS	Osteobl	bone
15	chr9:103360600-103362000	Active TSS	Rectal Smooth Muscle	rectum
16	chr9:103360800-103361600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:103360800-103361600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:103360800-103361600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr9:103360800-103361600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:103360800-103361600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:103360800-103361600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:103360800-103361600	Active TSS	Brain Cingulate Gyrus	brain
23	chr9:103360800-103361600	Active TSS	Brain Germinal Matrix	brain
24	chr9:103360800-103361600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr9:103360800-103361600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr9:103360800-103361600	Flanking Active TSS	Fetal Brain Male	brain
27	chr9:103360800-103361600	Active TSS	Fetal Brain Female	brain
28	chr9:103360800-103361600	Active TSS	Fetal Intestine Large	intestine
29	chr9:103360800-103361600	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr9:103360800-103361600	Flanking Active TSS	Fetal Thymus	thymus
31	chr9:103360800-103361600	Active TSS	Left Ventricle	heart
32	chr9:103360800-103361600	Active TSS	Ovary	ovary
33	chr9:103360800-103361600	Active TSS	Psoas Muscle	Psoas
34	chr9:103360800-103361600	Active TSS	Right Atrium	heart
35	chr9:103360800-103361600	Active TSS	Right Ventricle	heart
36	chr9:103360800-103361600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr9:103360800-103361600	Active TSS	HSMMtube	muscle
38	chr9:103360800-103361600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr9:103360800-103361600	Active TSS	NHDF-Ad	bronchial
40	chr9:103360800-103361800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:103360800-103361800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:103360800-103361800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr9:103360800-103361800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr9:103360800-103361800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr9:103360800-103361800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:103360800-103361800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:103360800-103361800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr9:103360800-103361800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:103360800-103361800	Active TSS	Fetal Kidney	kidney
50	chr9:103360800-103361800	Active TSS	Rectal Mucosa Donor 29	rectum

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