Variant report

Variant	rs12349359
Chromosome Location	chr9:27002512-27002513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10283643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1048949	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10511793	1.00[CHB][hapmap]
rs10812492	1.00[CHB][hapmap]
rs10812500	1.00[CHB][hapmap]
rs10967593	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10967594	1.00[CHB][hapmap]
rs10967595	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967624	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10967625	1.00[CHB][hapmap]
rs10967634	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10967638	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967639	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967640	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1161603	1.00[CHB][hapmap]
rs11788136	1.00[CHB][hapmap]
rs11999015	0.82[ASN][1000 genomes]
rs12001845	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12002068	0.82[ASN][1000 genomes]
rs12003612	0.82[ASN][1000 genomes]
rs12005388	1.00[CHB][hapmap]
rs12337860	1.00[CHB][hapmap]
rs12338678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12338827	0.82[ASN][1000 genomes]
rs12339063	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12339162	1.00[CHB][hapmap]
rs12340500	1.00[CHB][hapmap]
rs12342005	1.00[CHB][hapmap]
rs12343345	1.00[CHB][hapmap]
rs12345094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12352441	1.00[CHB][hapmap]
rs12352603	1.00[CHB][hapmap]
rs12352631	1.00[CHB][hapmap]
rs12554485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13293051	1.00[CHB][hapmap]
rs16910832	0.81[EUR][1000 genomes]
rs16910888	1.00[CHB][hapmap]
rs16910895	1.00[CHB][hapmap]
rs16911083	1.00[CHB][hapmap]
rs17694121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17694140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17694300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17694306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17694549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17694796	1.00[CHB][hapmap]
rs17755887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17755911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17756221	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17756599	1.00[CHB][hapmap]
rs17756667	1.00[CHB][hapmap]
rs17756685	1.00[CHB][hapmap]
rs2027124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2152063	1.00[CHB][hapmap]
rs28525632	0.93[EUR][1000 genomes]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs41271173	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41272237	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272239	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55902149	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59478807	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs59757728	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61331313	0.82[ASN][1000 genomes]
rs615532	1.00[CHB][hapmap]
rs6475948	1.00[CHB][hapmap]
rs6475959	1.00[CHB][hapmap]
rs6475963	1.00[CHB][hapmap]
rs6475966	1.00[CHB][hapmap]
rs6475968	1.00[CHB][hapmap]
rs7037860	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7039400	1.00[CHB][hapmap]
rs7040516	1.00[CHB][hapmap]
rs7040772	1.00[CHB][hapmap]
rs7042003	1.00[CHB][hapmap]
rs7042119	1.00[CHB][hapmap]
rs7042267	1.00[JPT][hapmap]
rs7044842	1.00[CHB][hapmap]
rs73433963	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73643117	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73643119	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73643120	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73643125	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73643128	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7847280	1.00[CHB][hapmap]
rs7854048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7871097	1.00[CHB][hapmap]
rs7871178	1.00[CHB][hapmap]
rs7871286	1.00[CHB][hapmap]
rs7873019	1.00[CHB][hapmap]
rs7873161	1.00[CHB][hapmap]
rs7873329	1.00[CHB][hapmap]

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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
2	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:26974200-27023600	Weak transcription	Fetal Brain Female	brain
5	chr9:26976200-27003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:26976800-27017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:26977200-27019400	Weak transcription	NH-A	brain
8	chr9:26977800-27026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:26979400-27024000	Weak transcription	Small Intestine	intestine
10	chr9:26982800-27023800	Weak transcription	Lung	lung
11	chr9:26983600-27023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:26985200-27011800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:26985200-27011800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:26985200-27015800	Weak transcription	Brain Angular Gyrus	brain
15	chr9:26985200-27016200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:26985200-27017400	Weak transcription	Brain Substantia Nigra	brain
17	chr9:26985200-27024000	Weak transcription	Right Ventricle	heart
18	chr9:26985200-27024000	Weak transcription	HSMM	muscle
19	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:26985400-27003400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:26985400-27004000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:26985400-27012200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:26985400-27012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:26985400-27013000	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:26985400-27015600	Weak transcription	Primary T cells from cord blood	blood
26	chr9:26985400-27015800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:26985400-27017400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:26985400-27017400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:26985400-27017800	Weak transcription	Fetal Thymus	thymus
30	chr9:26985400-27024000	Weak transcription	A549	lung
31	chr9:26985600-27024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:26985800-27018800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:26986000-27012200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:26986600-27004000	Weak transcription	Colonic Mucosa	Colon
35	chr9:26986800-27016000	Weak transcription	Ovary	ovary
36	chr9:26987200-27017200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:26987200-27023800	Weak transcription	HSMMtube	muscle
38	chr9:26987400-27019000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:26987400-27024000	Weak transcription	Aorta	Aorta
40	chr9:26987600-27012000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:26987800-27016000	Weak transcription	Adipose Nuclei	Adipose
42	chr9:26990800-27013000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:26991200-27003600	Weak transcription	Fetal Kidney	kidney
44	chr9:26991400-27017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:26991600-27016200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr9:26991600-27017400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
48	chr9:26992000-27010200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:26992800-27017200	Weak transcription	Fetal Stomach	stomach
50	chr9:26993000-27008600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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