Variant report

Variant	rs10208679
Chromosome Location	chr2:11894943-11894944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11886095..11889149-chr2:11892372..11895802,5	MCF-7	breast:
2	chr2:11894229..11895862-chr2:11899704..11901384,2	K562	blood:
3	chr2:11885383..11891655-chr2:11894666..11900002,13	K562	blood:
4	chr2:11893238..11895926-chr2:11901659..11904630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230790	Chromatin interaction
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006538	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10169802	0.99[ASN][1000 genomes]
rs10185333	0.88[AFR][1000 genomes]
rs10192566	0.99[ASN][1000 genomes]
rs10205312	0.89[ASN][1000 genomes]
rs10205400	0.88[ASN][1000 genomes]
rs10207506	1.00[ASN][1000 genomes]
rs10209969	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11676086	1.00[ASN][1000 genomes]
rs11693809	0.99[ASN][1000 genomes]
rs11897144	0.90[ASN][1000 genomes]
rs13407101	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13409154	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13412852	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469952	0.84[ASN][1000 genomes]
rs2278513	0.84[ASN][1000 genomes]
rs2358041	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358042	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4076055	0.99[ASN][1000 genomes]
rs4315495	1.00[ASN][1000 genomes]
rs4669778	0.83[ASN][1000 genomes]
rs62113306	0.96[ASN][1000 genomes]
rs6717910	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6731096	0.96[ASN][1000 genomes]
rs72773975	0.88[AFR][1000 genomes]
rs72773994	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7595221	0.93[ASN][1000 genomes]
rs873358	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893342	0.91[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:11888400-11895000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:11890400-11906400	Weak transcription	Fetal Brain Male	brain
4	chr2:11890600-11898600	Weak transcription	HepG2	liver
5	chr2:11890600-11905800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:11890800-11895600	Enhancers	Psoas Muscle	Psoas
7	chr2:11891000-11895200	Enhancers	HMEC	breast
8	chr2:11891400-11897400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:11891400-11903000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:11892200-11895200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr2:11892200-11895200	Enhancers	NHDF-Ad	bronchial
12	chr2:11892200-11895800	Enhancers	Small Intestine	intestine
13	chr2:11892800-11895000	Enhancers	Liver	Liver
14	chr2:11892800-11895000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:11892800-11895600	Enhancers	Fetal Thymus	thymus
16	chr2:11892800-11895800	Enhancers	Lung	lung
17	chr2:11893000-11895000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11893000-11895000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11893000-11895000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:11893000-11895000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:11893000-11895000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:11893000-11895000	Enhancers	Brain Hippocampus Middle	brain
23	chr2:11893000-11895000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:11893000-11895000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:11893000-11895000	Enhancers	Fetal Lung	lung
26	chr2:11893000-11895000	Enhancers	Gastric	stomach
27	chr2:11893000-11895000	Enhancers	Left Ventricle	heart
28	chr2:11893000-11895000	Enhancers	Pancreas	Pancrea
29	chr2:11893000-11895000	Enhancers	Right Ventricle	heart
30	chr2:11893000-11895000	Flanking Active TSS	GM12878-XiMat	blood
31	chr2:11893000-11895000	Enhancers	NHLF	lung
32	chr2:11893000-11895200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:11893000-11895200	Enhancers	Spleen	Spleen
34	chr2:11893200-11895000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:11893200-11895000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr2:11893200-11895000	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:11893400-11895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:11893400-11895000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:11893400-11895000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:11893400-11895000	Enhancers	Brain Angular Gyrus	brain
41	chr2:11893400-11895000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:11893600-11895000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:11893600-11895000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:11893600-11895000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr2:11893600-11895000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:11893600-11895000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:11893600-11895000	Enhancers	Fetal Stomach	stomach
48	chr2:11893600-11895000	Enhancers	Ovary	ovary
49	chr2:11893600-11895000	Enhancers	HSMM	muscle
50	chr2:11893600-11895000	Enhancers	HSMMtube	muscle

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