Variant report

Variant	rs11125519
Chromosome Location	chr2:54269386-54269387
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	chr2:54263866..54266283-chr2:54268179..54270997,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10084355	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10201364	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10203576	0.88[AMR][1000 genomes]
rs1058320	0.81[AMR][1000 genomes]
rs11683654	0.80[ASN][1000 genomes]
rs11687324	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12616212	0.82[EUR][1000 genomes]
rs12713253	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1363062	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1363063	0.91[AMR][1000 genomes]
rs1421617	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1421622	0.88[AMR][1000 genomes]
rs17268179	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2111868	0.81[AMR][1000 genomes]
rs2884254	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2909460	0.84[AMR][1000 genomes]
rs6545376	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545378	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6749817	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs698858	0.80[AMR][1000 genomes]
rs718872	0.82[AMR][1000 genomes]
rs7560947	0.81[AMR][1000 genomes]
rs7569214	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7569370	0.83[EUR][1000 genomes]
rs7571086	0.83[AMR][1000 genomes]
rs7591194	0.81[AMR][1000 genomes]
rs7609017	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805308	0.86[AMR][1000 genomes]
rs805309	0.86[AMR][1000 genomes]
rs805345	0.85[AMR][1000 genomes]
rs805359	0.82[AMR][1000 genomes]
rs805366	0.81[AMR][1000 genomes]
rs805367	0.82[AMR][1000 genomes]
rs805450	0.82[AMR][1000 genomes]
rs805453	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11125519	ACYP2	cis	Muscle Skeletal	GTEx
rs11125519	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
2	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
5	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
6	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:54258200-54269600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54258200-54269800	Weak transcription	Fetal Heart	heart
11	chr2:54258200-54269800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:54258200-54270000	Weak transcription	HepG2	liver
13	chr2:54260000-54269800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:54261200-54269600	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:54265200-54272400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:54265200-54272600	Enhancers	HMEC	breast
19	chr2:54266200-54269600	Weak transcription	Liver	Liver
20	chr2:54266200-54269800	Weak transcription	Aorta	Aorta
21	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
22	chr2:54266400-54271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:54266400-54271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:54266600-54269800	Weak transcription	A549	lung
25	chr2:54266800-54269600	Weak transcription	Brain Angular Gyrus	brain
26	chr2:54266800-54272200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:54267000-54272600	Weak transcription	Fetal Stomach	stomach
28	chr2:54267200-54270200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:54267400-54272000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:54267600-54269400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:54267600-54270000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:54267800-54271800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:54268000-54269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:54268000-54271400	Enhancers	Osteobl	bone
35	chr2:54268200-54269800	Weak transcription	Left Ventricle	heart
36	chr2:54268200-54270800	Strong transcription	Primary T cells from cord blood	blood
37	chr2:54268200-54275000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
39	chr2:54268400-54269600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:54268400-54270000	Weak transcription	Psoas Muscle	Psoas
41	chr2:54268400-54270800	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:54268600-54270000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:54268600-54270800	Weak transcription	NHEK	skin
46	chr2:54268600-54272400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:54268600-54275400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:54268800-54269400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:54268800-54275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:54268800-54275400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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