Variant report

Variant	rs2289889
Chromosome Location	chr8:120613822-120613823
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	chr8:120608131..120610098-chr8:120613256..120615439,2	K562	blood:
2	chr8:120612064..120614810-chr8:120616592..120619278,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10097147	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10097368	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10097501	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10098410	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110878	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10112316	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11991811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13277188	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374101	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326304	0.82[CEU][hapmap]
rs2875905	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2875906	0.82[CEU][hapmap]
rs3793378	0.82[CEU][hapmap]
rs4520196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4871360	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4871401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6469833	0.82[CEU][hapmap];0.88[MEX][hapmap]
rs6986760	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987232	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7007302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs755175	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7822457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823511	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9297599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs935360	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers 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	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2289889	ENPP2	cis	multi-tissue	Pritchard
rs2289889	ANXA2	trans	cerebellum	SCAN
rs2289889	MAL2	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120572200-120614200	Weak transcription	Fetal Intestine Large	intestine
2	chr8:120595600-120638000	Weak transcription	Fetal Muscle Leg	muscle
3	chr8:120595800-120633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:120595800-120637800	Weak transcription	Fetal Stomach	stomach
5	chr8:120597600-120634400	Weak transcription	Fetal Thymus	thymus
6	chr8:120599800-120614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr8:120600000-120617400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:120600000-120618000	Weak transcription	Brain Anterior Caudate	brain
9	chr8:120601800-120614600	Weak transcription	Osteobl	bone
10	chr8:120602000-120614000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:120602000-120627000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:120607000-120614000	Strong transcription	Adipose Nuclei	Adipose
13	chr8:120607800-120626600	Weak transcription	Liver	Liver
14	chr8:120609600-120614800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr8:120609800-120614200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:120609800-120617400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:120609800-120623600	Weak transcription	Placenta	Placenta
18	chr8:120610000-120614200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:120610000-120614800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr8:120610000-120614800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr8:120610000-120614800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr8:120610000-120614800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr8:120610000-120615000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr8:120610000-120618400	Weak transcription	Brain Angular Gyrus	brain
25	chr8:120610000-120621200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:120610200-120614800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr8:120610200-120614800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr8:120610200-120614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:120611000-120635400	Weak transcription	Colon Smooth Muscle	Colon
30	chr8:120611600-120614600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr8:120611800-120614000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr8:120611800-120614200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:120612400-120615400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr8:120612800-120614200	Strong transcription	Fetal Lung	lung
35	chr8:120613000-120623200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:120613200-120614200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
37	chr8:120613200-120614600	Enhancers	Primary B cells from peripheral blood	blood
38	chr8:120613200-120614600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr8:120613400-120614200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr8:120613400-120614400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:120613600-120614000	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr8:120613600-120614200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:120613600-120614200	Enhancers	Brain Hippocampus Middle	brain
44	chr8:120613600-120614200	Enhancers	Brain Substantia Nigra	brain
45	chr8:120613600-120615600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr8:120613600-120616000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr8:120613800-120614200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr8:120613800-120614400	Enhancers	GM12878-XiMat	blood
49	chr8:120613800-120620000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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