Variant report

Variant	rs11886664
Chromosome Location	chr2:11903840-11903841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
2	chr2:11893238..11895926-chr2:11901659..11904630,2	MCF-7	breast:
3	chr2:11902752..11905515-chr2:11914841..11917001,2	K562	blood:
4	chr2:11901357..11903016-chr2:11903554..11905723,2	MCF-7	breast:
5	chr2:11882411..11885202-chr2:11902345..11904670,2	K562	blood:
6	chr2:11883702..11885372-chr2:11901343..11903845,2	K562	blood:
7	chr2:11886543..11888583-chr2:11902069..11904944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10174816	1.00[CEU][hapmap]
rs10183250	1.00[EUR][1000 genomes]
rs11890221	1.00[EUR][1000 genomes]
rs11895768	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13420559	1.00[EUR][1000 genomes]
rs13421766	1.00[CEU][hapmap]
rs13424731	1.00[EUR][1000 genomes]
rs13431704	1.00[CEU][hapmap]
rs13432243	1.00[CEU][hapmap]
rs16857649	1.00[CEU][hapmap]
rs16857699	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16857866	1.00[MEX][hapmap]
rs4387757	1.00[CEU][hapmap]
rs55736020	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56187608	1.00[AMR][1000 genomes]
rs56352405	1.00[EUR][1000 genomes]
rs56820808	1.00[EUR][1000 genomes]
rs57779431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58686966	1.00[EUR][1000 genomes]
rs59101452	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59157966	1.00[EUR][1000 genomes]
rs59416046	1.00[EUR][1000 genomes]
rs59836200	1.00[EUR][1000 genomes]
rs61382095	1.00[EUR][1000 genomes]
rs61594850	1.00[AMR][1000 genomes]
rs6432217	1.00[CEU][hapmap]
rs6432218	1.00[CEU][hapmap]
rs6740248	1.00[CEU][hapmap]
rs6744817	1.00[CEU][hapmap]
rs6745921	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6757729	1.00[CEU][hapmap]
rs73185109	1.00[EUR][1000 genomes]
rs73915564	1.00[AMR][1000 genomes]
rs73917104	1.00[EUR][1000 genomes]
rs73917107	1.00[EUR][1000 genomes]
rs73917124	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73917127	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7562399	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7585718	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7602962	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:11890400-11906400	Weak transcription	Fetal Brain Male	brain
3	chr2:11890600-11905800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:11893800-11906400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:11894600-11904600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:11895000-11904400	Weak transcription	Adipose Nuclei	Adipose
7	chr2:11895000-11904400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:11895000-11904400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:11895000-11904600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:11895000-11904600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:11895000-11904600	Weak transcription	Hela-S3	cervix
12	chr2:11895000-11905000	Weak transcription	Gastric	stomach
13	chr2:11895000-11905400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:11895000-11905800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:11895000-11905800	Weak transcription	HSMMtube	muscle
16	chr2:11895000-11905800	Weak transcription	NH-A	brain
17	chr2:11895000-11905800	Weak transcription	Osteobl	bone
18	chr2:11895000-11906000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:11895000-11906200	Weak transcription	HSMM	muscle
20	chr2:11895000-11907000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:11895600-11905600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:11895800-11904600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:11895800-11905600	Weak transcription	NHDF-Ad	bronchial
25	chr2:11895800-11905800	Weak transcription	Spleen	Spleen
26	chr2:11897400-11905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:11897600-11909000	Weak transcription	Psoas Muscle	Psoas
28	chr2:11897800-11904400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11897800-11905000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:11898200-11905000	Weak transcription	GM12878-XiMat	blood
31	chr2:11898600-11906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:11899200-11905200	Weak transcription	Thymus	Thymus
33	chr2:11899200-11905400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:11899200-11906000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:11899200-11911200	Weak transcription	Small Intestine	intestine
36	chr2:11899400-11904200	Weak transcription	HepG2	liver
37	chr2:11899400-11905600	Weak transcription	Placenta	Placenta
38	chr2:11900600-11908800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:11900800-11905200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr2:11900800-11912200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:11901000-11904000	Genic enhancers	K562	blood
43	chr2:11901000-11905000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:11901000-11905400	Weak transcription	Brain Germinal Matrix	brain
45	chr2:11901000-11905400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:11901200-11904600	Weak transcription	Fetal Brain Female	brain
47	chr2:11901200-11909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:11901200-11915000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:11901400-11905600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:11901600-11904400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links