Variant report

Variant	rs12553901
Chromosome Location	chr9:21868757-21868758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10117507	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10965165	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10965168	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10965174	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10965175	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11526324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11531660	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11536713	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12236681	0.86[AMR][1000 genomes]
rs12236836	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238536	0.87[AMR][1000 genomes]
rs2027484	0.83[CEU][hapmap]
rs3802394	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4352938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4587423	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4607709	0.83[CEU][hapmap]
rs4977569	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4977735	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977736	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4977738	0.83[CEU][hapmap]
rs4977742	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4977743	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977744	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4977745	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56213153	0.85[AMR][1000 genomes]
rs62556506	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62556519	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62556520	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475592	0.83[CEU][hapmap]
rs7044807	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs756641	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7865071	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:21847600-21871600	Strong transcription	Dnd41	blood
3	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:21854200-21870200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:21854400-21869800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:21855400-21873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
10	chr9:21855800-21870600	Strong transcription	HMEC	breast
11	chr9:21856600-21871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:21857000-21871200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
14	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
16	chr9:21862200-21886800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:21862400-21874200	Weak transcription	Fetal Heart	heart
18	chr9:21863200-21880800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:21863800-21869800	Strong transcription	NH-A	brain
20	chr9:21863800-21870600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:21864200-21870000	Weak transcription	HUVEC	blood vessel
22	chr9:21864200-21870200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:21864200-21872000	Weak transcription	Stomach Mucosa	stomach
24	chr9:21864400-21871000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:21864400-21872600	Weak transcription	Fetal Intestine Small	intestine
26	chr9:21864800-21868800	Weak transcription	Aorta	Aorta
27	chr9:21864800-21868800	Weak transcription	Lung	lung
28	chr9:21864800-21869400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr9:21864800-21870200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:21864800-21875000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:21864800-21879400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr9:21865000-21869600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr9:21865000-21869600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:21865000-21870200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:21865000-21872200	Weak transcription	Esophagus	oesophagus
36	chr9:21865000-21873400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:21865000-21880800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:21865000-21890200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:21865200-21870200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:21865200-21870400	Weak transcription	Brain Germinal Matrix	brain
41	chr9:21865200-21870400	Weak transcription	Brain Substantia Nigra	brain
42	chr9:21865200-21870400	Weak transcription	Spleen	Spleen
43	chr9:21865200-21871200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:21865200-21875000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:21865400-21869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:21865400-21892600	Weak transcription	Colonic Mucosa	Colon
47	chr9:21865600-21869000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:21865600-21870200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:21865600-21870600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:21865600-21879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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