Variant report

Variant	rs12555830
Chromosome Location	chr9:17413173-17413174
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10810776	0.87[ASN][1000 genomes]
rs10963069	0.90[ASN][1000 genomes]
rs10963072	0.90[ASN][1000 genomes]
rs10963073	0.90[ASN][1000 genomes]
rs10963077	0.82[ASN][1000 genomes]
rs10963078	0.90[ASN][1000 genomes]
rs1160340	0.88[ASN][1000 genomes]
rs12156444	0.82[ASN][1000 genomes]
rs12553516	0.90[ASN][1000 genomes]
rs13285577	0.82[ASN][1000 genomes]
rs13285704	0.82[ASN][1000 genomes]
rs13286365	0.82[ASN][1000 genomes]
rs13289968	0.82[ASN][1000 genomes]
rs13294241	1.00[ASN][1000 genomes]
rs13298547	0.94[ASN][1000 genomes]
rs1442516	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1442517	0.82[ASN][1000 genomes]
rs2151342	0.87[ASN][1000 genomes]
rs2584538	0.88[ASN][1000 genomes]
rs36051199	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36088847	1.00[ASN][1000 genomes]
rs62558966	0.87[ASN][1000 genomes]
rs7019482	0.97[EUR][1000 genomes]
rs7028577	0.82[ASN][1000 genomes]
rs7031442	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv466271	chr9:17329964-17438391	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613696	chr9:17329964-17438391	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1015524	chr9:17350843-17419424	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv892668	chr9:17371690-17532840	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv892669	chr9:17378776-17438391	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892670	chr9:17378776-17507277	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466273	chr9:17391531-17436662	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv613697	chr9:17391531-17436662	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv523411	chr9:17394536-17454799	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12555830	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17381400-17422800	Weak transcription	Colon Smooth Muscle	Colon
3	chr9:17393400-17433000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr9:17395400-17413600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:17395400-17417800	Weak transcription	NHDF-Ad	bronchial
6	chr9:17396200-17413200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:17396200-17440000	Weak transcription	Adipose Nuclei	Adipose
8	chr9:17398800-17430600	Weak transcription	HSMM	muscle
9	chr9:17399400-17425400	Weak transcription	Fetal Heart	heart
10	chr9:17408000-17437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:17409600-17425400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:17411600-17428000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:17411800-17414000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:17411800-17416000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:17411800-17418200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:17411800-17423400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:17411800-17423400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:17411800-17428800	Weak transcription	Lung	lung
19	chr9:17411800-17429200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:17411800-17432200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:17411800-17434400	Weak transcription	Dnd41	blood
22	chr9:17411800-17435600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:17411800-17439800	Weak transcription	Left Ventricle	heart
24	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
25	chr9:17412000-17414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:17412000-17427600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:17412000-17428000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:17412200-17413800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:17412200-17418200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:17412200-17418400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:17412200-17419800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:17412200-17422800	Weak transcription	Fetal Lung	lung
33	chr9:17412200-17423000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:17412200-17424800	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:17412200-17425200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr9:17412200-17440200	Weak transcription	Fetal Stomach	stomach
37	chr9:17412200-17443600	Weak transcription	Ovary	ovary
38	chr9:17412400-17419600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr9:17412400-17430800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:17412600-17415600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links