Variant report

Variant	rs12568655
Chromosome Location	chr1:174434332-174434333
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	chr1:174427874..174429422-chr1:174431934..174434699,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10218528	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10753086	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10912773	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912797	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10912807	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10912824	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11804941	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs12060177	0.85[CEU][hapmap]
rs12074753	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs12077622	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs12084119	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs12088073	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs17301013	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2006197	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2038025	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2049991	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2049992	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs3737651	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs4650989	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs4650990	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs61826916	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6425279	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6425280	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6425281	0.84[CEU][hapmap]
rs6425282	0.84[CEU][hapmap];0.87[MEX][hapmap]
rs6425283	0.84[CEU][hapmap]
rs6425284	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6663591	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664864	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs6666767	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6668053	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6670617	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6671824	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6672148	0.84[CEU][hapmap]
rs6681780	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs6683602	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6693225	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs727279	0.83[CEU][hapmap];0.87[MEX][hapmap]
rs7512930	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7521870	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7523263	0.87[MEX][hapmap]
rs7523460	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7548540	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7552830	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7555067	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7555533	0.85[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv1003113	chr1:174367687-174499155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv535209	chr1:174367687-174499155	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	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
rs12568655	MRPS14	cis	parietal	SCAN
rs12568655	GPR52	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174381200-174438800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174415400-174444800	Weak transcription	Aorta	Aorta
3	chr1:174417800-174440800	Weak transcription	GM12878-XiMat	blood
4	chr1:174418000-174439000	Weak transcription	Left Ventricle	heart
5	chr1:174418000-174440000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:174430800-174445800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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