Variant report

Variant	rs11006281
Chromosome Location	chr10:52365541-52365542
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
2	chr10:52363840..52365627-chr10:52371839..52373893,2	K562	blood:
3	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17497064	0.94[ASN][1000 genomes]
rs3001879	0.95[ASN][1000 genomes]
rs3001883	0.95[ASN][1000 genomes]
rs3001885	0.95[ASN][1000 genomes]
rs3011714	0.95[ASN][1000 genomes]
rs4268459	0.97[ASN][1000 genomes]
rs4935735	1.00[ASN][1000 genomes]
rs4935737	0.94[ASN][1000 genomes]
rs4935739	0.97[ASN][1000 genomes]
rs6481442	0.98[ASN][1000 genomes]
rs6481461	0.95[ASN][1000 genomes]
rs7067552	0.98[ASN][1000 genomes]
rs7073182	0.96[ASN][1000 genomes]
rs7089882	0.92[ASN][1000 genomes]
rs7090996	0.97[ASN][1000 genomes]
rs7094655	0.98[ASN][1000 genomes]
rs7904101	0.97[ASN][1000 genomes]
rs7908136	0.99[ASN][1000 genomes]
rs7909486	0.98[ASN][1000 genomes]
rs7918559	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11006281	FLJ31958	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
2	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
4	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
5	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:52360000-52366200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr10:52360400-52366000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr10:52361600-52369000	Enhancers	Brain Anterior Caudate	brain
10	chr10:52362000-52368400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr10:52362000-52368400	Enhancers	Brain Substantia Nigra	brain
12	chr10:52362200-52367400	Enhancers	Brain Cingulate Gyrus	brain
13	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
14	chr10:52362400-52367200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr10:52362600-52365800	Enhancers	Fetal Intestine Small	intestine
16	chr10:52362600-52366800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr10:52362600-52368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:52362800-52365800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:52362800-52366000	Enhancers	Fetal Intestine Large	intestine
20	chr10:52362800-52366200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr10:52362800-52366200	Enhancers	Brain Angular Gyrus	brain
22	chr10:52362800-52366400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr10:52362800-52368000	Enhancers	HepG2	liver
24	chr10:52363000-52365800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr10:52363000-52365800	Enhancers	Small Intestine	intestine
26	chr10:52363000-52366000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr10:52363000-52368000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr10:52363200-52366000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:52363200-52366200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr10:52363200-52368000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:52363200-52368000	Enhancers	Stomach Mucosa	stomach
32	chr10:52363200-52371600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr10:52363400-52365600	Enhancers	Primary T cells from cord blood	blood
35	chr10:52363400-52365800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:52363400-52366200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:52363400-52366200	Enhancers	Adipose Nuclei	Adipose
38	chr10:52363400-52366200	Enhancers	NH-A	brain
39	chr10:52363400-52368000	Enhancers	Colon Smooth Muscle	Colon
40	chr10:52363600-52366000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:52363600-52366200	Flanking Active TSS	A549	lung
42	chr10:52363800-52365600	Enhancers	Fetal Kidney	kidney
43	chr10:52363800-52366600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr10:52363800-52367800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr10:52364000-52367200	Enhancers	Right Ventricle	heart
46	chr10:52364000-52367600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr10:52364000-52369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:52364200-52365600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr10:52364200-52365800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:52364200-52365800	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links