Variant report

Variant	rs897528
Chromosome Location	chr2:46949337-46949338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46924560..46926945-chr2:46947357..46950271,2	MCF-7	breast:
2	chr2:46944884..46947962-chr2:46948655..46951641,3	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1009230	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1009231	0.81[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10167561	0.96[ASN][1000 genomes]
rs10168342	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]
rs11125087	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12475080	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1456009	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1471056	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471057	0.84[ASN][1000 genomes]
rs1813505	0.96[ASN][1000 genomes]
rs1867819	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs2045291	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2061182	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3738890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3768720	0.88[MEX][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3814039	0.90[ASN][1000 genomes]
rs4361172	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4522653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953414	0.83[ASN][1000 genomes]
rs4953415	0.95[ASN][1000 genomes]
rs4953418	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6544913	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs6544917	0.85[ASN][1000 genomes]
rs6544918	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544919	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6544921	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705847	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6718658	0.83[YRI][hapmap]
rs6718677	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6721122	0.91[ASN][1000 genomes]
rs6726345	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6727737	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs6727934	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6728559	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6730949	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6740539	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs6741706	0.96[ASN][1000 genomes]
rs6746471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6748938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7568007	0.80[ASN][1000 genomes]
rs7570376	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580649	0.97[ASN][1000 genomes]
rs958726	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs970711	0.88[MEX][hapmap]
rs991742	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[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	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
7	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs897528	SOCS5	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46950800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:46945400-46952600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr2:46945400-46953400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:46946200-46949600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:46946600-46949600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:46946600-46951800	Enhancers	Colon Smooth Muscle	Colon
8	chr2:46946800-46953000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:46947000-46954600	Weak transcription	HUVEC	blood vessel
10	chr2:46947000-46954800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:46947600-46975600	Weak transcription	HSMM	muscle
12	chr2:46947800-46950800	Enhancers	Fetal Lung	lung
13	chr2:46947800-46952200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:46947800-46952600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:46948000-46951200	Weak transcription	Primary B cells from cord blood	blood
16	chr2:46948000-46954600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:46948000-46954600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:46948000-46954600	Weak transcription	Thymus	Thymus
19	chr2:46948200-46949400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:46948200-46949400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:46948200-46950000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:46948200-46950600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:46948200-46950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:46948200-46950600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:46948200-46950800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:46948200-46950800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:46948200-46950800	Enhancers	NHLF	lung
28	chr2:46948200-46951000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:46948200-46951400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:46948200-46951800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:46948200-46952400	Enhancers	NHDF-Ad	bronchial
32	chr2:46948200-46953000	Enhancers	A549	lung
33	chr2:46948200-46954400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:46948200-46954600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:46948200-46954600	Weak transcription	Left Ventricle	heart
36	chr2:46948200-46954600	Weak transcription	Right Ventricle	heart
37	chr2:46948200-46954800	Weak transcription	Pancreas	Pancrea
38	chr2:46948200-46955000	Weak transcription	Ovary	ovary
39	chr2:46948200-46955800	Weak transcription	Lung	lung
40	chr2:46948200-46956600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:46948200-46962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:46948200-46964400	Weak transcription	NHEK	skin
43	chr2:46948200-46967400	Weak transcription	Esophagus	oesophagus
44	chr2:46948200-46974600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
46	chr2:46948400-46949400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:46948400-46949400	Weak transcription	HepG2	liver
48	chr2:46948400-46949600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:46948400-46950800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:46948400-46950800	Weak transcription	GM12878-XiMat	blood

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