Variant report

Variant	rs718800
Chromosome Location	chr4:152549307-152549308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152547828..152549705-chr4:152551466..152554040,2	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10007653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10021407	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10022023	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026670	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033405	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107797	0.83[CEU][hapmap]
rs11099823	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11723395	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11723438	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729136	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732407	0.87[CHB][hapmap]
rs11736116	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11931934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932059	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932178	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11939356	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11940881	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941034	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11944139	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946622	0.95[EUR][1000 genomes]
rs12645029	1.00[CEU][hapmap]
rs12647566	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12648420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650655	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651635	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473305	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561916	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17275536	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17275577	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17275598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17360371	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17360385	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1822346	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1822347	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899549	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962910	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1978955	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2120098	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2165789	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406976	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407069	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724573	0.87[CHB][hapmap]
rs28454076	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28602726	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28608620	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235221	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696094	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696096	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696100	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696101	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696102	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696103	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696266	0.91[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696267	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696268	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696269	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696270	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696271	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696272	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696274	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696275	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696276	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696279	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696288	1.00[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4696289	1.00[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs55808836	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932132	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55977324	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56319216	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62327266	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62327267	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327268	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327269	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327270	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327271	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327274	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327275	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327349	0.81[EUR][1000 genomes]
rs62327350	0.80[EUR][1000 genomes]
rs62329084	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62329087	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62329088	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62329090	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62329091	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62329092	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62329101	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535806	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66852535	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6831810	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6833814	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836249	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6836343	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839802	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6853955	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6858483	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72728173	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72728179	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72728182	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72730104	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664663	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7678080	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7685697	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689266	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695412	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs875668	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9884167	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9884486	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs718800	PET112L	cis	parietal	SCAN
rs718800	FAM160A1	cis	cerebellum	SCAN
rs718800	PET112L	cis	cerebellum	SCAN
rs718800	PLRG1	cis	cerebellum	SCAN
rs718800	LRBA	cis	cerebellum	SCAN
rs718800	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152499200-152567600	Weak transcription	Pancreas	Pancrea
2	chr4:152522400-152560200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:152542400-152565600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:152544000-152570600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:152544200-152566400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:152544400-152570600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152545600-152578600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:152546000-152550800	Weak transcription	Lung	lung
9	chr4:152546400-152550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:152546400-152552800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:152546400-152561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:152546400-152570600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:152547400-152550600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:152548200-152558800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:152548400-152549400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:152548400-152549400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:152548400-152549600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:152548400-152550200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:152548600-152550000	Enhancers	NHDF-Ad	bronchial
20	chr4:152548800-152558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:152549000-152549600	Enhancers	Fetal Heart	heart
22	chr4:152549000-152567000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:152549200-152550800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:152549200-152561600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:152549200-152562000	Weak transcription	NHEK	skin

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