Variant report

Variant	rs12775180
Chromosome Location	chr10:116639754-116639755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10444099	1.00[JPT][hapmap]
rs1045657	1.00[JPT][hapmap]
rs1046492	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510007	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10885633	1.00[JPT][hapmap]
rs10885634	1.00[JPT][hapmap]
rs10885636	1.00[JPT][hapmap]
rs10885638	1.00[JPT][hapmap]
rs10885639	1.00[JPT][hapmap]
rs11196963	1.00[CHB][hapmap]
rs11196984	1.00[JPT][hapmap]
rs11196996	1.00[JPT][hapmap]
rs11196999	1.00[JPT][hapmap]
rs11197000	1.00[JPT][hapmap]
rs11197007	1.00[JPT][hapmap]
rs11197010	1.00[JPT][hapmap]
rs11197012	1.00[JPT][hapmap]
rs11818115	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	1.00[JPT][hapmap]
rs12265048	1.00[JPT][hapmap]
rs12269261	1.00[JPT][hapmap]
rs12761122	1.00[JPT][hapmap]
rs12764662	1.00[JPT][hapmap]
rs12765350	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092497	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721905	1.00[JPT][hapmap]
rs17794346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[JPT][hapmap]
rs1966384	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	1.00[JPT][hapmap]
rs2146806	1.00[ASN][1000 genomes]
rs3180654	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34064819	1.00[ASN][1000 genomes]
rs34187191	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683721	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010779	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284358	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60820172	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867966	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867967	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61868018	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[JPT][hapmap]
rs6585310	1.00[JPT][hapmap]
rs6585311	1.00[JPT][hapmap]
rs68085797	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071789	1.00[JPT][hapmap]
rs7071812	1.00[JPT][hapmap]
rs7072356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072364	1.00[ASN][1000 genomes]
rs7074729	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089973	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7093674	1.00[ASN][1000 genomes]
rs7094072	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[JPT][hapmap]
rs7099590	1.00[JPT][hapmap]
rs7100026	1.00[JPT][hapmap]
rs749649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898249	1.00[JPT][hapmap]
rs7904605	1.00[JPT][hapmap]
rs7908069	1.00[JPT][hapmap]
rs7908464	1.00[JPT][hapmap]
rs7909566	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918253	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881192	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:116617400-116640600	Weak transcription	Fetal Intestine Small	intestine
4	chr10:116619400-116641600	Weak transcription	Aorta	Aorta
5	chr10:116635200-116640600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:116636800-116641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:116637000-116639800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:116637000-116639800	Weak transcription	Ovary	ovary
9	chr10:116637000-116640400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:116637000-116640400	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:116637000-116641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:116637000-116641400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:116637000-116641400	Weak transcription	Stomach Mucosa	stomach
14	chr10:116637000-116641400	Weak transcription	HSMMtube	muscle
15	chr10:116637000-116641600	Weak transcription	NHEK	skin
16	chr10:116637000-116641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:116637000-116641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:116637000-116641800	Weak transcription	NH-A	brain
19	chr10:116637000-116642200	Weak transcription	HMEC	breast
20	chr10:116637200-116639800	Weak transcription	Placenta	Placenta
21	chr10:116638600-116641600	Weak transcription	Right Atrium	heart
22	chr10:116638800-116639800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr10:116638800-116640600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr10:116638800-116641400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:116639000-116639800	Enhancers	Adipose Nuclei	Adipose
26	chr10:116639000-116639800	Enhancers	Liver	Liver
27	chr10:116639000-116639800	Enhancers	A549	lung
28	chr10:116639000-116640000	Enhancers	Dnd41	blood
29	chr10:116639000-116642000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:116639000-116643000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr10:116639200-116639800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:116639200-116639800	Weak transcription	Fetal Lung	lung
33	chr10:116639200-116639800	Enhancers	Thymus	Thymus
34	chr10:116639200-116639800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr10:116639200-116640000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr10:116639200-116640000	Enhancers	Primary hematopoietic stem cells	blood
37	chr10:116639200-116640000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:116639200-116640000	Enhancers	HepG2	liver
39	chr10:116639200-116640200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr10:116639200-116640800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr10:116639200-116642200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr10:116639200-116642800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr10:116639400-116639800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr10:116639400-116639800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:116639400-116639800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:116639400-116639800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:116639400-116639800	Enhancers	Lung	lung
48	chr10:116639400-116639800	Enhancers	Pancreas	Pancrea
49	chr10:116639400-116640000	Enhancers	Primary T cells from cord blood	blood
50	chr10:116639400-116640000	Enhancers	Brain Germinal Matrix	brain

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