Variant report

Variant	rs170768
Chromosome Location	chr1:174689925-174689926
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	chr1:174688388..174690592-chr1:174693450..174696212,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10753086	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs10912807	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs10912824	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11804941	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs12060177	0.85[CEU][hapmap]
rs12074753	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs12088073	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs1653626	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs1653627	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs1653632	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs1754351	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs1754355	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap]
rs1793291	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1793293	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793297	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs1793319	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1894200	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2038025	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2187562	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap]
rs2987869	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs2987874	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap]
rs3018410	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs3118980	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs3133270	0.85[CEU][hapmap]
rs332765	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs332783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332794	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332795	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs332796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332799	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333418	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233195	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap]
rs4650666	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs61826916	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425284	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs6425305	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs6658861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6664864	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs6671824	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap]
rs6672148	0.85[CEU][hapmap]
rs6683602	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs6688577	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6693225	0.84[EUR][1000 genomes]
rs67276708	0.83[ASN][1000 genomes]
rs7521870	0.80[EUR][1000 genomes]
rs7538588	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs7538650	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555533	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs913685	0.84[EUR][1000 genomes];0.82[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	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs170768	GPR52	cis	parietal	SCAN
rs170768	MRPS14	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174678200-174708600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:174678600-174706400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:174682200-174704800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:174687800-174705200	Weak transcription	Primary B cells from cord blood	blood
5	chr1:174689000-174695400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:174689000-174695800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:174689600-174691000	Enhancers	HepG2	liver
8	chr1:174689800-174690200	Enhancers	Fetal Heart	heart
9	chr1:174689800-174690800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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