Variant report

Variant	rs11887593
Chromosome Location	chr2:54267775-54267776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54265196..54267933-chr2:54270964..54273028,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10181332	0.90[EUR][1000 genomes]
rs10188834	0.83[AMR][1000 genomes]
rs10190353	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193846	0.92[EUR][1000 genomes]
rs10199995	1.00[AMR][1000 genomes]
rs10496027	0.91[AFR][1000 genomes]
rs1049894	0.88[AMR][1000 genomes]
rs11125517	0.83[AMR][1000 genomes]
rs11884857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886366	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11889527	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11903396	0.91[AFR][1000 genomes]
rs11904365	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13382454	0.89[AFR][1000 genomes]
rs13395751	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13401491	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	0.83[AMR][1000 genomes]
rs13417051	0.88[AMR][1000 genomes]
rs13432387	0.88[AMR][1000 genomes]
rs2112120	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161083	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571698	1.00[AMR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.81[AFR][1000 genomes]
rs41536750	0.88[AMR][1000 genomes]
rs58920915	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60769690	0.83[AMR][1000 genomes]
rs60776154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545382	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711310	0.85[AFR][1000 genomes]
rs6715161	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6719990	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6723722	0.94[AMR][1000 genomes]
rs6730494	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6745729	0.88[AMR][1000 genomes]
rs6748686	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751340	0.83[AMR][1000 genomes]
rs72904915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906704	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906711	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906714	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906778	0.92[EUR][1000 genomes]
rs72906786	0.92[EUR][1000 genomes]
rs72906787	0.92[EUR][1000 genomes]
rs7556936	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	1.00[AMR][1000 genomes]
rs7583508	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588134	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588319	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608085	0.88[AMR][1000 genomes]
rs9678301	0.88[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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54243800-54268000	Weak transcription	Osteobl	bone
2	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
7	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:54258200-54269600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:54258200-54269800	Weak transcription	Fetal Heart	heart
13	chr2:54258200-54269800	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:54258200-54270000	Weak transcription	HepG2	liver
15	chr2:54260000-54269800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:54261200-54269600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:54262000-54268200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:54264200-54268200	Weak transcription	Primary T cells from cord blood	blood
21	chr2:54265200-54272400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:54265200-54272600	Enhancers	HMEC	breast
23	chr2:54266200-54269600	Weak transcription	Liver	Liver
24	chr2:54266200-54269800	Weak transcription	Aorta	Aorta
25	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:54266400-54267800	Enhancers	Psoas Muscle	Psoas
27	chr2:54266400-54268000	Weak transcription	NHEK	skin
28	chr2:54266400-54271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:54266400-54271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:54266600-54269800	Weak transcription	A549	lung
31	chr2:54266800-54269600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:54266800-54272200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:54267000-54268000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:54267000-54272600	Weak transcription	Fetal Stomach	stomach
35	chr2:54267200-54267800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:54267200-54267800	Enhancers	Adipose Nuclei	Adipose
37	chr2:54267200-54270200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:54267400-54268400	Enhancers	Brain Substantia Nigra	brain
39	chr2:54267400-54272000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:54267600-54268200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:54267600-54269000	Weak transcription	Ovary	ovary
42	chr2:54267600-54269400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:54267600-54270000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links