Variant report

Variant	rs17415195
Chromosome Location	chr3:155443852-155443853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155443638..155446622-chr3:155570722..155573140,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169359	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17349490	0.82[GIH][hapmap];0.82[TSI][hapmap]
rs17349560	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415343	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213840	1.00[ASN][1000 genomes]
rs57149264	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227176	1.00[ASN][1000 genomes]
rs6765861	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782387	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156584	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156598	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156600	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156602	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159011	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159017	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159021	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159025	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159026	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73159032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73159054	1.00[ASN][1000 genomes]
rs73159063	1.00[ASN][1000 genomes]
rs73873405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615287	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs7615938	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617878	1.00[ASN][1000 genomes]
rs7621415	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641701	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648978	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757945	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9882341	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17415195	SLC33A1	cis	cerebellum	SCAN
rs17415195	SLC33A1	cis	parietal	SCAN
rs17415195	RARRES1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155432400-155461600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:155436600-155447000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:155438400-155448800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:155438600-155444800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:155439200-155455600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:155440200-155446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:155441400-155444000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:155441600-155448800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:155442000-155454200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:155443800-155444400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:155443800-155444400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:155443800-155444400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:155443800-155447000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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