Variant report

Variant	rs2961581
Chromosome Location	chr10:4878204-4878205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:4867479..4869815-chr10:4877781..4879971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165568	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10736992	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1078063	0.95[AFR][1000 genomes]
rs10795203	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10795204	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10904352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904356	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252777	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252779	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11252780	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11252781	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252782	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252784	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252785	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11252786	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11252787	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11252788	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11252789	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11252790	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11252794	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11252795	0.84[EUR][1000 genomes]
rs11528590	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12761251	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12761278	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12778158	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12779835	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12779887	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12780592	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1869218	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1869221	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1901644	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1993181	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2123353	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2123354	0.92[AFR][1000 genomes]
rs2167703	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2397981	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2397984	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2924264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2924265	0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2924267	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2961568	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2961571	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs2961576	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2961578	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2961586	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2961589	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2961591	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2961592	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2961593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2961596	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3110959	0.83[AFR][1000 genomes]
rs35035905	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35588485	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4268414	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4357596	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4359096	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4385791	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4405202	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4405203	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4537666	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4565807	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4881354	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4881358	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4881359	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4881360	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4881361	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4881362	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4881364	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7067785	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7076172	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7084200	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7088294	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7091514	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7099392	0.95[AMR][1000 genomes];0.95[EUR][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	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4868800-4879800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:4869000-4881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:4869200-4883600	Weak transcription	Thymus	Thymus
4	chr10:4869200-4884800	Weak transcription	Esophagus	oesophagus
5	chr10:4869200-4889200	Weak transcription	NHLF	lung
6	chr10:4869200-4889600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:4869200-4890400	Weak transcription	Right Atrium	heart
8	chr10:4869200-4891600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:4869200-4892200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:4869400-4878400	Weak transcription	Placenta	Placenta
11	chr10:4869400-4879000	Weak transcription	Fetal Lung	lung
12	chr10:4869400-4883400	Weak transcription	Colonic Mucosa	Colon
13	chr10:4869400-4886800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:4869400-4889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:4869400-4889600	Weak transcription	HSMM	muscle
16	chr10:4869400-4891600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:4869600-4878600	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:4869600-4883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:4869600-4885000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:4869600-4889200	Weak transcription	HUVEC	blood vessel
21	chr10:4869600-4889600	Weak transcription	NHEK	skin
22	chr10:4869800-4880600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:4869800-4884800	Weak transcription	Right Ventricle	heart
24	chr10:4869800-4885800	Weak transcription	Stomach Mucosa	stomach
25	chr10:4870200-4879600	Weak transcription	Fetal Heart	heart
26	chr10:4870600-4886200	Weak transcription	Small Intestine	intestine
27	chr10:4870600-4887800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr10:4870600-4891800	Weak transcription	Fetal Brain Male	brain
29	chr10:4872400-4889200	Weak transcription	NHDF-Ad	bronchial
30	chr10:4872600-4889200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr10:4872600-4892400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:4872800-4882200	Weak transcription	Liver	Liver
33	chr10:4872800-4886600	Strong transcription	A549	lung
34	chr10:4873000-4880000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr10:4873000-4880200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:4873000-4880200	Strong transcription	Aorta	Aorta
37	chr10:4873000-4880600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:4873000-4880600	Strong transcription	Adipose Nuclei	Adipose
39	chr10:4873000-4881200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:4873000-4887000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr10:4873000-4887600	Strong transcription	Fetal Muscle Leg	muscle
42	chr10:4873200-4879800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:4873200-4880600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr10:4873400-4879800	Strong transcription	Fetal Stomach	stomach
45	chr10:4873400-4880600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr10:4873400-4885600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr10:4874200-4881000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:4874600-4880200	Strong transcription	Spleen	Spleen
49	chr10:4874600-4891800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr10:4875000-4880600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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