Variant report

Variant	rs937960
Chromosome Location	chr15:39976057-39976058
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39879533..39881128-chr15:39975849..39978589,2	MCF-7	breast:
2	chr15:39974204..39976528-chr15:39982397..39984405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1105159	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs11070231	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11631820	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11631824	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12050804	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12899323	0.88[ASN][1000 genomes]
rs12900024	0.84[ASN][1000 genomes]
rs12900583	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12901142	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs12903514	0.89[ASN][1000 genomes]
rs12911549	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12911999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1906152	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1906155	0.92[ASN][1000 genomes]
rs1906156	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994379	0.91[CHB][hapmap]
rs2129459	0.93[ASN][1000 genomes]
rs2411299	0.90[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs2411300	1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2411301	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2411304	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2411307	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411308	0.88[ASN][1000 genomes]
rs2411309	0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2411310	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2411311	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2411312	0.80[MEX][hapmap]
rs2631694	0.83[CEU][hapmap];0.85[GIH][hapmap]
rs2631697	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2631700	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs2631701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2631702	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631704	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631705	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631710	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2631711	0.83[CEU][hapmap]
rs2664125	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2664129	0.85[GIH][hapmap]
rs2664132	0.83[GIH][hapmap]
rs2664133	0.93[ASN][1000 genomes]
rs2664135	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]
rs28437905	0.89[ASN][1000 genomes]
rs28581473	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2898685	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3103065	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4319738	0.94[ASN][1000 genomes]
rs4429263	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4476148	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480779	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4493017	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4505280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4572354	0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4591113	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4606692	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4924376	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4924377	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492909	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6492910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492911	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs68183224	0.93[ASN][1000 genomes]
rs7167100	0.89[ASN][1000 genomes]
rs7171939	0.80[GIH][hapmap]
rs7177857	0.93[ASN][1000 genomes]
rs7179013	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs8033902	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs8034543	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034885	0.89[ASN][1000 genomes]
rs8035354	0.93[ASN][1000 genomes]
rs8036226	0.89[ASN][1000 genomes]
rs8042068	0.89[ASN][1000 genomes]
rs951358	0.91[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9672572	0.91[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	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	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs937960	CASC5	cis	parietal	SCAN
rs937960	VPS18	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39972600-39976400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:39972600-39978800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:39972800-39977000	Enhancers	Muscle Satellite Cultured Cells	--
4	chr15:39973400-39982800	Weak transcription	Fetal Lung	lung
5	chr15:39973800-39982800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:39974200-39978400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:39974800-39985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:39975000-39978000	Weak transcription	HSMM	muscle
9	chr15:39975000-39978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:39975400-39976800	Weak transcription	NHDF-Ad	bronchial
11	chr15:39975400-39976800	Weak transcription	Osteobl	bone
12	chr15:39975400-39977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:39975400-39982000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:39975400-39984400	Weak transcription	Fetal Kidney	kidney
15	chr15:39975600-39977000	Weak transcription	HSMMtube	muscle
16	chr15:39975600-39978000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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