Variant report

Variant	rs11265544
Chromosome Location	chr1:161006019-161006020
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161004664..161006659-chr1:161007054..161009588,2	MCF-7	breast:
2	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
3	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
4	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270149	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11588189	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116949	0.82[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap]
rs12130871	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2516838	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774279	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34339899	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35925761	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892375	1.00[JPT][hapmap];1.00[LWK][hapmap]
rs4656974	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11265544	FCGR2A	cis	parietal	SCAN
rs11265544	FCRL1	cis	cerebellum	SCAN
rs11265544	PVRL4	cis	parietal	SCAN
rs11265544	ITLN1	cis	cerebellum	SCAN
rs11265544	OR10K1	cis	cerebellum	SCAN
rs11265544	F11R	cis	cerebellum	SCAN
rs11265544	TSTD1,F11R	cis	cerebellar cortex	BrainEAC
rs11265544	SNORA42	cis	cerebellum	SCAN
rs11265544	KIRREL	cis	parietal	SCAN
rs11265544	TSTD1,F11R	cis	brain	BrainEAC

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160991200-161007800	Weak transcription	HSMMtube	muscle
2	chr1:160991600-161007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:160991800-161007600	Weak transcription	Thymus	Thymus
4	chr1:160991800-161007800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:160992000-161007000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:160992200-161008000	Weak transcription	HUVEC	blood vessel
7	chr1:160997200-161008000	Weak transcription	A549	lung
8	chr1:161001800-161006800	Weak transcription	Lung	lung
9	chr1:161001800-161007800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:161002000-161007600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:161002200-161007600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:161002600-161007400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:161002800-161007200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:161003000-161007000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:161003000-161007000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:161003000-161007200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:161003000-161007400	Weak transcription	GM12878-XiMat	blood
18	chr1:161003000-161008200	Weak transcription	Osteobl	bone
19	chr1:161003200-161006800	Weak transcription	HepG2	liver
20	chr1:161003200-161007000	Weak transcription	Liver	Liver
21	chr1:161003200-161007200	Weak transcription	Fetal Heart	heart
22	chr1:161003200-161007400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:161003200-161007600	Weak transcription	HSMM	muscle
24	chr1:161003200-161007800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:161003200-161008800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:161003800-161006800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:161003800-161007000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:161003800-161007000	Weak transcription	Adipose Nuclei	Adipose
29	chr1:161003800-161007400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:161003800-161007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:161004000-161007000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:161004000-161007000	Weak transcription	NHEK	skin
33	chr1:161004000-161007200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:161004000-161007600	Weak transcription	HMEC	breast
35	chr1:161004000-161009200	Weak transcription	Hela-S3	cervix
36	chr1:161004200-161007000	Weak transcription	Placenta	Placenta
37	chr1:161004200-161008000	Weak transcription	Spleen	Spleen
38	chr1:161004400-161007000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:161005000-161007000	Weak transcription	Brain Germinal Matrix	brain
40	chr1:161005000-161007200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:161005000-161007200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:161005000-161007400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:161005000-161007600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:161005000-161009400	Weak transcription	K562	blood
45	chr1:161005200-161007000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:161005200-161007000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:161005200-161007200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:161005200-161007200	Weak transcription	Fetal Stomach	stomach
49	chr1:161005200-161007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:161005200-161007600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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