Variant report

Variant	rs12339675
Chromosome Location	chr9:14206835-14206836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14198598..14200536-chr9:14204416..14206854,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10119190	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756540	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10756541	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810116	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810117	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10961428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12551619	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7040930	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic 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	5 gene(s)	inside rSNPs	diseases
7	nsv892596	chr9:14145487-14208724	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv892597	chr9:14163383-14233159	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12339675	KIAA0913	trans	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14192800-14207400	Weak transcription	Spleen	Spleen
2	chr9:14192800-14213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:14199000-14209200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:14199200-14209600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:14199400-14207400	Weak transcription	Esophagus	oesophagus
6	chr9:14199400-14207400	Weak transcription	Gastric	stomach
7	chr9:14199400-14209400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:14199400-14215800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:14200200-14207200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:14200200-14207400	Weak transcription	Lung	lung
11	chr9:14201200-14220000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:14203000-14212000	Weak transcription	Fetal Intestine Small	intestine
13	chr9:14203800-14207000	Weak transcription	Brain Germinal Matrix	brain
14	chr9:14203800-14207400	Weak transcription	Brain Anterior Caudate	brain
15	chr9:14203800-14207800	Enhancers	Osteobl	bone
16	chr9:14203800-14209600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:14203800-14211600	Weak transcription	HSMMtube	muscle
18	chr9:14203800-14214200	Weak transcription	Brain Substantia Nigra	brain
19	chr9:14203800-14217200	Enhancers	Fetal Heart	heart
20	chr9:14203800-14219000	Weak transcription	Ovary	ovary
21	chr9:14203800-14221800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:14204000-14209000	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:14204000-14211800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:14204000-14213000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:14204000-14221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:14204200-14211600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:14204400-14208200	Enhancers	Liver	Liver
28	chr9:14204400-14208800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:14204400-14209000	Weak transcription	Fetal Brain Male	brain
30	chr9:14204600-14207400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:14204600-14208000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:14204800-14207200	Weak transcription	Psoas Muscle	Psoas
33	chr9:14204800-14207200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:14204800-14207400	Weak transcription	Aorta	Aorta
35	chr9:14204800-14208000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:14204800-14208000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:14204800-14208000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:14204800-14208000	Enhancers	HMEC	breast
39	chr9:14205000-14207200	Weak transcription	Pancreas	Pancrea
40	chr9:14205000-14207400	Weak transcription	Left Ventricle	heart
41	chr9:14205000-14207400	Weak transcription	Right Atrium	heart
42	chr9:14205000-14208200	Enhancers	NHEK	skin
43	chr9:14205400-14207000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:14205400-14207600	Enhancers	Fetal Brain Female	brain
45	chr9:14205400-14208000	Enhancers	Adipose Nuclei	Adipose
46	chr9:14205400-14208000	Enhancers	Colon Smooth Muscle	Colon
47	chr9:14205400-14208200	Enhancers	HSMM	muscle
48	chr9:14205600-14207600	Enhancers	Fetal Lung	lung
49	chr9:14205600-14208000	Enhancers	Right Ventricle	heart
50	chr9:14205800-14207000	Weak transcription	Rectal Smooth Muscle	rectum

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