Variant report

Variant	rs2631702
Chromosome Location	chr15:40000071-40000072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39881585..39883327-chr15:39998681..40000213,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1105159	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11070231	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs11631820	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11631824	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12050804	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12899323	0.84[ASN][1000 genomes]
rs12900024	0.80[ASN][1000 genomes]
rs12900583	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12901142	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12903514	0.86[ASN][1000 genomes]
rs12911549	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12911999	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs1906152	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1906155	0.93[ASN][1000 genomes]
rs1906156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1994379	0.95[CHB][hapmap]
rs2129459	0.92[ASN][1000 genomes]
rs2411299	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2411300	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[ASN][1000 genomes]
rs2411301	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2411304	0.81[ASN][1000 genomes]
rs2411307	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2411308	0.86[ASN][1000 genomes]
rs2411309	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2411310	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2411311	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2631694	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2631697	0.86[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631700	0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs2631701	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631704	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631705	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];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631710	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2664125	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2664126	0.85[CEU][hapmap]
rs2664129	0.94[CEU][hapmap];0.90[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs2664132	0.94[CEU][hapmap];0.87[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2664133	0.94[ASN][1000 genomes]
rs2664135	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]
rs28437905	0.86[ASN][1000 genomes]
rs28581473	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2898685	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3103065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4319738	0.91[ASN][1000 genomes]
rs4429263	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4476148	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4480779	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4493017	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4505280	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4572354	0.93[ASW][hapmap];0.88[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];0.84[MKK][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4591113	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4606692	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4924376	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924377	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492909	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6492910	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492911	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs68183224	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165067	0.81[CHB][hapmap]
rs7167100	0.86[ASN][1000 genomes]
rs7171939	0.81[ASW][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap]
rs7177857	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7179013	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs8033902	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs8034543	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8034885	0.85[ASN][1000 genomes]
rs8035354	0.90[ASN][1000 genomes]
rs8036226	0.86[ASN][1000 genomes]
rs8042068	0.87[ASN][1000 genomes]
rs937960	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]
rs951358	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9672572	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2631702	CASC5	cis	parietal	SCAN
rs2631702	VPS18	cis	parietal	SCAN
rs2631702	GPR176	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39997000-40001800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:39997400-40000800	Weak transcription	NHDF-Ad	bronchial
3	chr15:39997600-40000800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:39997600-40002400	Weak transcription	Osteobl	bone
5	chr15:39999800-40004400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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