Variant report

Variant	rs7179293
Chromosome Location	chr15:39900774-39900775
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39899166..39901640-chr15:39907361..39909302,2	MCF-7	breast:
2	chr15:39899512..39901195-chr15:39903262..39904844,2	MCF-7	breast:
3	chr15:39879443..39881394-chr15:39898682..39901295,2	MCF-7	breast:
4	chr15:39892971..39897381-chr15:39898907..39901655,6	MCF-7	breast:
5	chr15:39896909..39899758-chr15:39899972..39902669,2	K562	blood:
6	chr15:39873532..39876107-chr15:39899045..39902121,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10152640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10520137	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10520138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10520142	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11070220	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070221	0.92[ASN][1000 genomes]
rs11070222	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11070223	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11070224	0.92[ASN][1000 genomes]
rs11070225	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1134485	0.80[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1134486	0.84[ASN][1000 genomes]
rs11630406	0.81[CHB][hapmap]
rs11631820	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs11631824	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs11632879	0.81[CHB][hapmap]
rs11635103	0.81[CHB][hapmap]
rs11852591	0.80[CHB][hapmap]
rs11852649	0.81[CHB][hapmap]
rs11856971	0.80[CHB][hapmap]
rs11857819	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12050804	0.84[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12443011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12900583	0.85[EUR][1000 genomes]
rs12908846	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs12912082	0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1478604	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1478605	0.82[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16969386	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16969395	0.94[ASN][1000 genomes]
rs16969410	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16969459	0.81[CHB][hapmap]
rs16969475	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs16969478	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1876852	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1876853	0.81[CHB][hapmap]
rs1904209	0.85[ASN][1000 genomes]
rs2169830	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2228261	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2229364	0.84[ASN][1000 genomes]
rs2292305	0.85[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2411310	0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2411313	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2411314	0.85[JPT][hapmap]
rs2411315	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412412	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412413	0.81[CHB][hapmap]
rs2412415	0.81[CHB][hapmap]
rs2412417	0.80[CHB][hapmap]
rs2412418	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412419	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2412420	0.92[ASN][1000 genomes]
rs2412421	0.87[ASN][1000 genomes]
rs2618162	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2618163	0.94[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2664139	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2664141	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2898686	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2898687	0.81[CHB][hapmap]
rs2898688	0.81[CHB][hapmap]
rs3743125	0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs4319738	0.87[EUR][1000 genomes]
rs4319740	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4349120	0.81[CHB][hapmap]
rs4429263	0.81[EUR][1000 genomes]
rs4493017	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs4505280	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs4547308	0.80[CHB][hapmap]
rs4583211	0.80[JPT][hapmap]
rs56938133	0.92[ASN][1000 genomes]
rs66781090	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67239630	0.92[ASN][1000 genomes]
rs7162070	0.81[CHB][hapmap]
rs7162781	0.81[CHB][hapmap]
rs7167366	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168755	0.81[CHB][hapmap]
rs7169574	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7170335	0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs7170682	0.89[ASN][1000 genomes]
rs7176721	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs7177324	0.89[ASN][1000 genomes]
rs7180675	0.80[AMR][1000 genomes]
rs7183544	0.81[ASN][1000 genomes]
rs753598	0.81[ASN][1000 genomes]
rs753599	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs768663	0.84[GIH][hapmap]
rs8029602	0.81[CHB][hapmap]
rs8032035	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs8034594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035354	0.83[EUR][1000 genomes]
rs8036376	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8036633	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs8039035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs884584	0.81[JPT][hapmap]
rs9302102	0.81[ASN][1000 genomes]
rs949646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964424	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs970280	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806365	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9806647	0.89[ASN][1000 genomes]
rs999393	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7179293	CASC5	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39888400-39901000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:39888400-39901000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:39889200-39901200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:39890200-39900800	Weak transcription	HMEC	breast
5	chr15:39899600-39901000	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr15:39899600-39901400	Weak transcription	Esophagus	oesophagus
7	chr15:39899600-39901600	Weak transcription	Left Ventricle	heart
8	chr15:39899800-39901000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr15:39900200-39904600	Weak transcription	HUVEC	blood vessel
10	chr15:39900400-39902200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links