Variant report

Variant	rs59444417
Chromosome Location	chr2:98553571-98553572
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98528410..98530497-chr2:98551746..98553885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238719	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs55853292	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55887737	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58415781	0.93[AMR][1000 genomes]
rs58690282	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59049638	0.83[EUR][1000 genomes]
rs59635122	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs59752876	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60567628	0.81[AFR][1000 genomes]
rs61363543	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154513	0.85[AMR][1000 genomes]
rs62154549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154552	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62154553	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62154555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62154556	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62154558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62156480	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62156482	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62156488	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156508	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156514	0.90[EUR][1000 genomes]
rs62156519	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62156522	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156523	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156524	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156525	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156526	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62156527	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156530	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62157630	0.93[AMR][1000 genomes]
rs62158265	0.83[EUR][1000 genomes]
rs62158266	0.89[EUR][1000 genomes]
rs62158268	0.89[EUR][1000 genomes]
rs62158269	0.83[EUR][1000 genomes]
rs62158270	0.89[EUR][1000 genomes]
rs62158272	0.89[EUR][1000 genomes]
rs73960406	0.81[AFR][1000 genomes]
rs73960407	0.81[AFR][1000 genomes]
rs73960426	0.81[AFR][1000 genomes]
rs73960430	0.83[AFR][1000 genomes]
rs73960433	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73960435	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7420897	0.93[AMR][1000 genomes]
rs7575922	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7600204	0.83[EUR][1000 genomes]
rs7606272	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98544400-98554400	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:98545800-98554000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr2:98547400-98554000	Enhancers	Fetal Lung	lung
4	chr2:98549800-98553800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:98549800-98554000	Enhancers	NHDF-Ad	bronchial
6	chr2:98550000-98553600	Enhancers	Liver	Liver
7	chr2:98550000-98554000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:98550200-98554200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:98550400-98553800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:98550400-98554200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:98550800-98553600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:98550800-98553600	Enhancers	Brain Hippocampus Middle	brain
13	chr2:98550800-98553800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:98550800-98554000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:98551000-98553800	Enhancers	Brain Anterior Caudate	brain
16	chr2:98551400-98553800	Enhancers	Adipose Nuclei	Adipose
17	chr2:98551400-98554000	Enhancers	Stomach Mucosa	stomach
18	chr2:98551600-98554000	Enhancers	Dnd41	blood
19	chr2:98551800-98553600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:98551800-98554000	Enhancers	Primary B cells from cord blood	blood
21	chr2:98552000-98553600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:98552000-98554200	Enhancers	Osteobl	bone
23	chr2:98552200-98553600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:98552200-98553600	Enhancers	Fetal Brain Female	brain
25	chr2:98552200-98553800	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:98552200-98553800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:98552200-98553800	Enhancers	Brain Angular Gyrus	brain
28	chr2:98552200-98553800	Flanking Active TSS	GM12878-XiMat	blood
29	chr2:98552200-98553800	Enhancers	HepG2	liver
30	chr2:98552200-98554000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:98552200-98554000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:98552400-98553800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:98552400-98553800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:98552400-98553800	Enhancers	Fetal Brain Male	brain
35	chr2:98552400-98553800	Enhancers	Fetal Stomach	stomach
36	chr2:98552400-98554000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr2:98552400-98554200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:98552600-98553800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:98552800-98553600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:98552800-98553600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:98553000-98553600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:98553000-98554000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:98553000-98559600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:98553000-98561600	Weak transcription	Primary T cells from cord blood	blood
45	chr2:98553200-98553600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:98553200-98553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:98553200-98565800	Weak transcription	Small Intestine	intestine
48	chr2:98553400-98553600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:98553400-98553600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:98553400-98553800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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