Variant report

Variant	rs10168342
Chromosome Location	chr2:46932523-46932524
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	chr2:46925096..46927639-chr2:46929889..46935400,5	MCF-7	breast:
2	chr2:46930029..46933528-chr2:46976256..46980348,3	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1009230	0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1009231	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10167561	0.92[ASN][1000 genomes]
rs11125087	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12466948	0.80[ASN][1000 genomes]
rs12475080	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1456009	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1471056	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471057	0.87[ASN][1000 genomes]
rs1809216	0.80[ASN][1000 genomes]
rs1813505	0.93[ASN][1000 genomes]
rs1867819	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs2045291	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2061182	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3738890	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3768720	0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814039	0.87[ASN][1000 genomes]
rs4361172	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4522653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953414	0.87[ASN][1000 genomes]
rs4953415	0.91[ASN][1000 genomes]
rs4953418	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6544913	0.82[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6544917	0.89[ASN][1000 genomes]
rs6544918	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544919	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6544921	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6705847	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6718658	0.83[YRI][hapmap]
rs6718677	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721122	0.87[ASN][1000 genomes]
rs6726345	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6727737	0.83[CEU][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6727934	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6728559	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6730949	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6740539	0.85[YRI][hapmap]
rs6741706	0.93[ASN][1000 genomes]
rs6746471	0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6748938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568007	0.83[ASN][1000 genomes]
rs7570376	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580649	0.95[ASN][1000 genomes]
rs897528	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958726	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs991559	0.81[ASN][1000 genomes]
rs991742	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46927200-46935800	Weak transcription	Spleen	Spleen
2	chr2:46927400-46933400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:46927400-46933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46927600-46932800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
7	chr2:46928600-46933600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:46928600-46933600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr2:46928600-46934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:46928800-46932600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:46928800-46932600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:46928800-46932600	Enhancers	HepG2	liver
14	chr2:46928800-46932800	Weak transcription	HSMMtube	muscle
15	chr2:46928800-46933400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:46928800-46933800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:46928800-46934400	Enhancers	NH-A	brain
18	chr2:46928800-46938600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:46928800-46946200	Weak transcription	NHEK	skin
20	chr2:46929000-46940200	Weak transcription	Fetal Stomach	stomach
21	chr2:46929200-46934400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:46929400-46933400	Weak transcription	Hela-S3	cervix
23	chr2:46929400-46933400	Weak transcription	HMEC	breast
24	chr2:46929400-46933600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:46929600-46934600	Enhancers	Colon Smooth Muscle	Colon
26	chr2:46930000-46934000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:46930000-46934600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:46930000-46934600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:46930000-46938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:46930200-46934400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:46930400-46933400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:46930400-46936400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:46930600-46932800	Weak transcription	Fetal Lung	lung
34	chr2:46930600-46933000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:46931000-46932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr2:46931000-46932600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:46931200-46934200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:46931200-46938800	Weak transcription	Primary B cells from cord blood	blood
39	chr2:46931400-46932600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:46931400-46932600	Enhancers	Psoas Muscle	Psoas
41	chr2:46931400-46933200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr2:46931400-46933200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:46931400-46933200	Genic enhancers	NHDF-Ad	bronchial
44	chr2:46931400-46934000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:46931400-46935600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:46931600-46932600	Enhancers	Stomach Mucosa	stomach
47	chr2:46931600-46932800	Enhancers	Brain Cingulate Gyrus	brain
48	chr2:46931600-46933000	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:46931600-46933600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:46931600-46934400	Enhancers	H9 Cell Line	embryonic stem cell

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