Variant report

Variant	rs2276554
Chromosome Location	chr2:46807991-46807992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46806489..46808552-chr2:46842875..46845193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151665	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1057899	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs1060656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11306	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11901678	0.97[ASN][1000 genomes]
rs11903907	0.90[ASN][1000 genomes]
rs13404342	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13410076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs1376406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1456010	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1456018	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17035272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17035361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1809087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3213985	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768724	0.90[ASN][1000 genomes]
rs3768725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4377377	0.97[ASN][1000 genomes]
rs57134465	0.97[ASN][1000 genomes]
rs57955462	0.97[ASN][1000 genomes]
rs58101879	0.97[ASN][1000 genomes]
rs58342271	0.90[ASN][1000 genomes]
rs59183773	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59823825	0.90[ASN][1000 genomes]
rs60211996	0.97[ASN][1000 genomes]
rs60738814	0.90[ASN][1000 genomes]
rs61252474	0.97[ASN][1000 genomes]
rs6544904	0.97[ASN][1000 genomes]
rs6544908	0.82[ASN][1000 genomes]
rs6713104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6719813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6727471	0.97[ASN][1000 genomes]
rs6733143	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6735530	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs6756134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs68104662	0.90[ASN][1000 genomes]
rs72875696	0.90[ASN][1000 genomes]
rs7563577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7589908	0.97[ASN][1000 genomes]
rs7591561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7592446	0.90[ASN][1000 genomes]
rs962467	0.90[ASN][1000 genomes]
rs9808496	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2276554	CRIPT	cis	lymphoblastoid	seeQTL
rs2276554	PIGF	cis	lymphoblastoid	seeQTL
rs2276554	SLC3A1	cis	parietal	SCAN
rs2276554	MYEOV	trans	lymphoblastoid	seeQTL
rs2276554	CRIPT	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
3	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
6	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
8	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:46796600-46822000	Weak transcription	Fetal Brain Male	brain
10	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
11	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:46797800-46814400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:46797800-46841000	Weak transcription	K562	blood
14	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:46801200-46808400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:46801200-46815000	Weak transcription	Psoas Muscle	Psoas
17	chr2:46802400-46815000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:46802400-46842600	Weak transcription	NHEK	skin
19	chr2:46802600-46809600	Strong transcription	Fetal Thymus	thymus
20	chr2:46802800-46837000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:46803200-46810800	Weak transcription	Brain Angular Gyrus	brain
22	chr2:46803400-46808000	Strong transcription	A549	lung
23	chr2:46803400-46810600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:46803400-46811600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:46803400-46811800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:46803400-46811800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:46803400-46818800	Weak transcription	HepG2	liver
28	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:46803600-46809200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:46803600-46811800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:46803600-46811800	Strong transcription	Osteobl	bone
32	chr2:46803800-46808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:46803800-46808400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:46803800-46808600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:46803800-46810600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:46803800-46811800	Strong transcription	Adipose Nuclei	Adipose
37	chr2:46804000-46810400	Weak transcription	HUVEC	blood vessel
38	chr2:46804200-46812200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:46804400-46811400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:46805200-46808200	Strong transcription	NHDF-Ad	bronchial
41	chr2:46805400-46808000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:46805400-46808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:46805400-46808600	Strong transcription	NH-A	brain
44	chr2:46805600-46815600	Weak transcription	Fetal Lung	lung
45	chr2:46805600-46836400	Weak transcription	HSMM	muscle
46	chr2:46806000-46811000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:46806200-46808000	Enhancers	Fetal Heart	heart
48	chr2:46806200-46810800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:46806400-46808000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:46806400-46808000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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