Variant report

Variant	rs2664135
Chromosome Location	chr15:40012164-40012165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40004259..40006236-chr15:40010388..40013115,2	MCF-7	breast:
2	chr15:40011583..40013446-chr15:40013529..40016434,2	MCF-7	breast:
3	chr15:39991017..39993549-chr15:40010029..40012182,2	K562	blood:
4	chr15:40011315..40014662-chr15:40074849..40076901,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1105159	0.95[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs11070231	0.85[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs11631820	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11631824	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12050804	0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12899323	0.83[ASN][1000 genomes]
rs12900583	0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12901142	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12903514	0.84[ASN][1000 genomes]
rs12911549	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12911999	0.90[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs1906152	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1906155	0.91[ASN][1000 genomes]
rs1906156	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994379	1.00[CHB][hapmap]
rs2129459	0.91[ASN][1000 genomes]
rs2411299	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2411300	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.90[ASN][1000 genomes]
rs2411301	0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2411307	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2411308	0.84[ASN][1000 genomes]
rs2411309	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2411310	0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2411311	0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2631694	0.83[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2631697	0.81[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2631700	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631701	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2631702	0.93[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631704	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631705	0.93[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631710	0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2664125	0.94[ASN][1000 genomes]
rs2664129	0.88[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2664132	0.85[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2664133	0.92[ASN][1000 genomes]
rs28437905	0.84[ASN][1000 genomes]
rs28581473	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2898685	0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs3103065	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs4319738	0.88[ASN][1000 genomes]
rs4429263	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4476148	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4480779	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4493017	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4505280	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4572354	1.00[ASW][hapmap];0.93[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];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4591113	0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs4606692	0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924376	0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4924377	0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6492909	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6492910	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6492911	0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs68183224	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165067	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7167100	0.84[ASN][1000 genomes]
rs7171939	0.82[GIH][hapmap];0.92[MKK][hapmap]
rs7177857	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179013	0.91[CHB][hapmap]
rs8033902	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs8034543	0.88[ASN][1000 genomes]
rs8034885	0.84[ASN][1000 genomes]
rs8035354	0.87[ASN][1000 genomes]
rs8036226	0.84[ASN][1000 genomes]
rs8042068	0.85[ASN][1000 genomes]
rs937960	0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs951358	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9672572	0.88[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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh 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 target site	63 gene(s)	inside rSNPs	diseases
6	esv20190	chr15:40009652-40012222	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv14441	chr15:40011435-40012222	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2664135	VPS18	cis	parietal	SCAN
rs2664135	CASC5	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40009000-40012600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:40011000-40014400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:40011000-40014800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:40011200-40012800	Enhancers	Placenta	Placenta
5	chr15:40011200-40012800	Enhancers	Osteobl	bone
6	chr15:40011200-40013200	Enhancers	NHEK	skin
7	chr15:40011200-40013400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:40011600-40013600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:40011600-40013600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:40011600-40014000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr15:40011800-40012400	Enhancers	Fetal Lung	lung
12	chr15:40011800-40012800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:40011800-40012800	Enhancers	NHDF-Ad	bronchial
14	chr15:40011800-40013800	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:40011800-40014400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40012000-40014400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:40012000-40014400	Enhancers	HMEC	breast

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