Variant report

Variant	rs10121012
Chromosome Location	chr9:15554265-15554266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10116904	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117524	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117803	0.83[AMR][1000 genomes]
rs10117823	0.83[AMR][1000 genomes]
rs10118595	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118675	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118719	0.94[EUR][1000 genomes]
rs10119257	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119931	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120171	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121911	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121971	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123084	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123651	0.83[AMR][1000 genomes]
rs10124655	0.92[EUR][1000 genomes]
rs10124718	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124746	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125713	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1041529	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962054	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962061	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336383	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12336445	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337310	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344963	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348561	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348564	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350062	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352398	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12353048	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12859	0.92[AMR][1000 genomes]
rs1509311	0.83[AMR][1000 genomes]
rs175762	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848583	0.83[AMR][1000 genomes]
rs1882939	0.83[EUR][1000 genomes]
rs202321	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2064030	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2202865	1.00[ASN][1000 genomes]
rs2221706	0.91[AMR][1000 genomes]
rs2382536	0.83[AMR][1000 genomes]
rs2665503	0.97[EUR][1000 genomes]
rs2665510	0.83[EUR][1000 genomes]
rs2665511	0.83[EUR][1000 genomes]
rs2665512	0.83[EUR][1000 genomes]
rs2665515	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2737840	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276434	1.00[ASN][1000 genomes]
rs276437	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276438	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276439	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276440	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs276442	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs276445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276446	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276451	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276452	0.82[EUR][1000 genomes]
rs2777951	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2795123	0.83[EUR][1000 genomes]
rs2795124	0.83[EUR][1000 genomes]
rs2795125	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2795127	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2795128	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798717	0.83[AMR][1000 genomes]
rs2821525	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821529	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821530	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2821533	0.83[EUR][1000 genomes]
rs2821542	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821543	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821544	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449490	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497163	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610358	0.97[EUR][1000 genomes]
rs28659858	0.91[AMR][1000 genomes]
rs28735068	0.91[EUR][1000 genomes]
rs28796681	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28800775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28805077	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28808908	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28844368	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28882210	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28893033	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119700	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122701	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3122705	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129711	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365710	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381205	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392627	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs398117	1.00[ASN][1000 genomes]
rs398178	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs399808	1.00[ASN][1000 genomes]
rs401393	1.00[ASN][1000 genomes]
rs413356	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415157	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418153	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237140	0.91[AMR][1000 genomes]
rs424131	1.00[ASN][1000 genomes]
rs443563	0.91[EUR][1000 genomes]
rs4445326	0.83[AMR][1000 genomes]
rs592452	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474941	0.83[AMR][1000 genomes]
rs6474943	0.83[AMR][1000 genomes]
rs7021840	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741930	0.92[AMR][1000 genomes]
rs7852936	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860339	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796391	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811282	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909323	0.83[EUR][1000 genomes]
rs926154	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298729	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9406518	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15551800-15554400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:15551800-15554400	Active TSS	Brain Angular Gyrus	brain
3	chr9:15551800-15554400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr9:15551800-15554400	Active TSS	Fetal Brain Female	brain
5	chr9:15551800-15554600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:15551800-15554600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr9:15552000-15554400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:15552000-15554400	Active TSS	Thymus	Thymus
9	chr9:15552000-15554600	Active TSS	NHDF-Ad	bronchial
10	chr9:15552200-15554400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr9:15552200-15554400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:15552200-15554400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr9:15552200-15554400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:15552200-15554400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:15552200-15554600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:15552200-15554600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:15552200-15554600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr9:15552200-15554600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:15552200-15554600	Active TSS	Brain Anterior Caudate	brain
20	chr9:15552200-15554600	Active TSS	Fetal Kidney	kidney
21	chr9:15552400-15554600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr9:15552600-15554400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:15553200-15555000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:15553600-15554800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:15553800-15554400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:15553800-15554400	Enhancers	Fetal Muscle Leg	muscle
27	chr9:15553800-15554400	Active TSS	Placenta	Placenta
28	chr9:15553800-15554400	Weak transcription	Pancreas	Pancrea
29	chr9:15553800-15554600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:15553800-15554600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:15553800-15554600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr9:15553800-15554600	Enhancers	K562	blood
33	chr9:15553800-15576200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:15553800-15580600	Weak transcription	Ovary	ovary
35	chr9:15553800-15592600	Weak transcription	Left Ventricle	heart
36	chr9:15554000-15554400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr9:15554000-15554400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr9:15554000-15554400	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr9:15554000-15554400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:15554000-15554400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:15554000-15554400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:15554000-15554400	Enhancers	Fetal Lung	lung
43	chr9:15554000-15554400	Enhancers	Fetal Muscle Trunk	muscle
44	chr9:15554000-15554400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr9:15554000-15554600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr9:15554000-15554600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr9:15554000-15554600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:15554000-15554600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr9:15554000-15554600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:15554000-15554600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links