Variant report

Variant	rs4873143
Chromosome Location	chr8:51202721-51202722
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	chr8:51194558..51197541-chr8:51202196..51204695,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10092399	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10094935	0.84[CHD][hapmap]
rs10103047	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs10108468	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs10113812	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs10504099	0.93[CHB][hapmap]
rs10808817	0.85[CHB][hapmap]
rs10957853	0.92[CHB][hapmap]
rs1117213	0.92[JPT][hapmap]
rs1160764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783674	0.87[ASN][1000 genomes]
rs11784464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784719	1.00[CHB][hapmap]
rs12056425	0.93[CHB][hapmap]
rs12056426	0.93[CHB][hapmap]
rs12541382	1.00[CEU][hapmap]
rs12541772	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12544473	1.00[CHB][hapmap]
rs12545003	0.83[JPT][hapmap]
rs12545915	0.93[CHB][hapmap]
rs12545927	1.00[CHB][hapmap]
rs12677964	0.91[CHB][hapmap]
rs12678703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12679356	0.93[CHB][hapmap]
rs12680748	1.00[CHB][hapmap]
rs12681918	0.90[ASN][1000 genomes]
rs13248969	1.00[CHB][hapmap]
rs13249415	0.85[CHB][hapmap]
rs13251725	1.00[CHB][hapmap]
rs13252320	0.92[CHB][hapmap]
rs13253758	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs13257851	0.83[JPT][hapmap]
rs13260021	1.00[CHB][hapmap]
rs13260265	0.83[CHD][hapmap]
rs13260288	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs13275607	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs13282956	0.92[CHB][hapmap]
rs1349316	0.93[CHB][hapmap]
rs1349317	0.85[CHB][hapmap]
rs1375944	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1375945	1.00[CHB][hapmap]
rs1375947	0.90[ASN][1000 genomes]
rs1375948	1.00[CHB][hapmap]
rs1380789	1.00[CHB][hapmap]
rs1380790	0.91[CHB][hapmap]
rs1380791	1.00[CHB][hapmap]
rs1380792	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1450124	1.00[ASW][hapmap];0.96[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]
rs1450132	1.00[CHB][hapmap]
rs1450135	0.84[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1460437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1481471	0.83[JPT][hapmap]
rs1597426	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1597427	0.90[ASN][1000 genomes]
rs1597428	0.93[CHB][hapmap]
rs1597430	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs1597431	0.93[CHB][hapmap]
rs1597432	0.92[JPT][hapmap]
rs1597433	0.92[JPT][hapmap]
rs16914346	0.83[CHD][hapmap]
rs16914780	0.83[JPT][hapmap]
rs17770910	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1824462	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1868638	0.90[ASN][1000 genomes]
rs1868639	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1901055	0.93[CHB][hapmap]
rs1901056	1.00[CHB][hapmap]
rs1947254	0.92[JPT][hapmap]
rs2167157	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2219574	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2840054	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28510664	0.85[ASN][1000 genomes]
rs2957598	0.92[JPT][hapmap]
rs34217744	0.80[ASN][1000 genomes]
rs34651805	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34788367	0.83[ASN][1000 genomes]
rs35516514	0.80[ASN][1000 genomes]
rs35857674	0.85[ASN][1000 genomes]
rs3919764	0.88[ASN][1000 genomes]
rs4256602	0.92[JPT][hapmap]
rs4330704	0.85[CHB][hapmap]
rs4339654	0.92[JPT][hapmap]
rs4398931	0.93[CHB][hapmap]
rs4410921	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4448284	0.93[CHB][hapmap];0.84[CHD][hapmap]
rs4534138	0.92[JPT][hapmap]
rs4543555	0.93[CHB][hapmap]
rs4577969	0.93[CHB][hapmap]
rs4604450	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs4618709	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4633068	0.93[CHB][hapmap]
rs4873141	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4873142	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs4873438	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4873439	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4873442	0.85[CHB][hapmap]
rs4873443	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4873447	1.00[CHB][hapmap]
rs4873451	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs4873452	0.90[ASN][1000 genomes]
rs62515888	0.88[ASN][1000 genomes]
rs6981805	0.85[CHB][hapmap]
rs6989084	0.90[ASN][1000 genomes]
rs6990514	0.90[ASN][1000 genomes]
rs6999627	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs7003725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005672	0.92[JPT][hapmap]
rs7015950	0.91[JPT][hapmap]
rs7017642	0.85[CHB][hapmap]
rs7464491	0.93[CHB][hapmap]
rs7821189	0.85[CHB][hapmap]
rs7822367	0.90[ASN][1000 genomes]
rs7822550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834452	0.90[ASN][1000 genomes]
rs7835144	0.86[ASN][1000 genomes]
rs7839253	0.92[JPT][hapmap]
rs9643720	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs968944	0.92[CHB][hapmap]
rs968945	1.00[CHB][hapmap]
rs968947	1.00[CHB][hapmap]

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	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv470212	chr8:51176635-51227506	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4873143	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51201800-51202800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:51202600-51202800	Enhancers	H9 Cell Line	embryonic stem cell

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