Variant report

Variant	rs1065778
Chromosome Location	chr15:51520206-51520207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51511082..51513770-chr15:51518994..51521491,2	K562	blood:
2	chr15:51518976..51520763-chr15:51526661..51528605,2	MCF-7	breast:
3	chr15:51515145..51517510-chr15:51519278..51520848,2	MCF-7	breast:
4	chr15:51514557..51518713-chr15:51518929..51521836,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10046	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10459592	0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10519297	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1062033	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1065779	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10851498	0.83[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851499	0.88[ASN][1000 genomes]
rs1143704	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11632036	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633715	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636403	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11636667	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636686	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856927	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12050772	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12148604	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12591172	0.92[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12899068	0.88[ASN][1000 genomes]
rs12900487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901187	0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12907866	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12908960	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12917091	0.82[EUR][1000 genomes]
rs17523270	0.83[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17523284	0.83[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289105	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2304463	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414096	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28757200	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28757202	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899470	0.83[TSI][hapmap]
rs2899471	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35241865	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35808887	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784307	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3825800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4324076	1.00[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4545755	0.86[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4774583	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775932	0.87[EUR][1000 genomes]
rs4775936	0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56097510	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61018102	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493488	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493489	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493494	0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs700518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167936	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176330	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180552	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs767199	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023263	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8029120	0.92[CEU][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8034835	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8041967	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1065778	USP8	cis	cerebellum	SCAN
rs1065778	TMOD2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51513200-51520400	Weak transcription	HepG2	liver
2	chr15:51515200-51520400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:51515200-51521000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr15:51515200-51521600	Enhancers	NHDF-Ad	bronchial
5	chr15:51515400-51520600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:51516400-51520400	Weak transcription	Aorta	Aorta
7	chr15:51516800-51520400	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:51517000-51520400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:51517200-51520400	Weak transcription	Brain Anterior Caudate	brain
10	chr15:51518200-51520400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:51518400-51521400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:51518600-51520400	Enhancers	K562	blood
13	chr15:51518800-51520400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:51518800-51520400	Enhancers	Fetal Brain Female	brain
15	chr15:51519400-51521400	Enhancers	NHLF	lung
16	chr15:51519600-51520800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr15:51519600-51521200	Enhancers	HMEC	breast
18	chr15:51519600-51521400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:51520000-51520400	Enhancers	A549	lung
20	chr15:51520000-51520400	Enhancers	NH-A	brain
21	chr15:51520000-51520600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:51520000-51520800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr15:51520000-51520800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr15:51520000-51520800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr15:51520000-51520800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:51520000-51520800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:51520000-51520800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:51520000-51521000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:51520000-51521000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr15:51520000-51521000	Genic enhancers	Placenta	Placenta
31	chr15:51520000-51521000	Enhancers	NHEK	skin
32	chr15:51520000-51521200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr15:51520000-51521200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:51520000-51521200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr15:51520000-51521200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:51520000-51521200	Enhancers	Hela-S3	cervix
37	chr15:51520000-51521200	Enhancers	HSMM	muscle
38	chr15:51520000-51521200	Enhancers	HUVEC	blood vessel
39	chr15:51520000-51521400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:51520200-51520400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:51520200-51520600	Enhancers	Small Intestine	intestine
42	chr15:51520200-51520800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr15:51520200-51520800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr15:51520200-51520800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:51520200-51520800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:51520200-51520800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr15:51520200-51520800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr15:51520200-51520800	Flanking Active TSS	GM12878-XiMat	blood
49	chr15:51520200-51520800	Flanking Active TSS	HSMMtube	muscle
50	chr15:51520200-51520800	Flanking Active TSS	Osteobl	bone

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