Variant report

Variant	rs62060550
Chromosome Location	chr16:75502252-75502253
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	chr16:75499072..75501045-chr16:75501380..75504166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs100912	0.86[ASN][1000 genomes]
rs1030261	0.97[ASN][1000 genomes]
rs1030262	0.98[ASN][1000 genomes]
rs10871311	0.80[ASN][1000 genomes]
rs10871312	0.97[ASN][1000 genomes]
rs10871313	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149831	0.80[ASN][1000 genomes]
rs11641249	0.96[ASN][1000 genomes]
rs11641430	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11641801	0.80[ASN][1000 genomes]
rs11643207	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644306	0.97[ASN][1000 genomes]
rs11644639	0.80[ASN][1000 genomes]
rs11648176	0.80[ASN][1000 genomes]
rs11649638	0.97[ASN][1000 genomes]
rs11865296	0.83[ASN][1000 genomes]
rs12051137	0.95[ASN][1000 genomes]
rs12149063	0.80[ASN][1000 genomes]
rs12444589	0.80[ASN][1000 genomes]
rs12446877	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12448829	0.87[ASN][1000 genomes]
rs12918797	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924333	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12927562	0.96[ASN][1000 genomes]
rs12928036	0.96[ASN][1000 genomes]
rs12929673	0.81[ASN][1000 genomes]
rs12932606	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12933281	0.96[ASN][1000 genomes]
rs1424013	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542864	0.81[ASN][1000 genomes]
rs17696831	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834013	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834014	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161684	0.94[ASN][1000 genomes]
rs247454	0.88[ASN][1000 genomes]
rs2738809	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2738812	0.82[ASN][1000 genomes]
rs2738813	0.82[ASN][1000 genomes]
rs2738814	0.83[ASN][1000 genomes]
rs28558946	0.97[ASN][1000 genomes]
rs2865528	0.80[ASN][1000 genomes]
rs28655617	0.95[ASN][1000 genomes]
rs3115960	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34021527	0.85[ASN][1000 genomes]
rs34539062	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918083	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996006	0.93[ASN][1000 genomes]
rs35209155	0.81[ASN][1000 genomes]
rs35214308	0.93[ASN][1000 genomes]
rs35683383	0.94[ASN][1000 genomes]
rs37592	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37593	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37594	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37595	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37597	0.92[ASN][1000 genomes]
rs37599	0.82[ASN][1000 genomes]
rs37602	0.82[ASN][1000 genomes]
rs37605	0.81[ASN][1000 genomes]
rs37606	0.96[ASN][1000 genomes]
rs40446	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887825	0.81[ASN][1000 genomes]
rs4887829	0.97[ASN][1000 genomes]
rs4888415	0.80[ASN][1000 genomes]
rs4888425	0.93[ASN][1000 genomes]
rs4888426	0.93[ASN][1000 genomes]
rs4888427	0.94[ASN][1000 genomes]
rs4888430	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888431	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888432	0.87[ASN][1000 genomes]
rs56004344	0.86[ASN][1000 genomes]
rs56116092	0.94[ASN][1000 genomes]
rs59155720	0.94[ASN][1000 genomes]
rs59347518	0.92[ASN][1000 genomes]
rs59465235	0.96[ASN][1000 genomes]
rs62060551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564261	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188604	0.80[ASN][1000 genomes]
rs7191890	0.83[ASN][1000 genomes]
rs7193828	0.89[ASN][1000 genomes]
rs7194035	0.89[ASN][1000 genomes]
rs7195161	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198873	0.92[ASN][1000 genomes]
rs7199062	0.93[ASN][1000 genomes]
rs7199132	0.80[ASN][1000 genomes]
rs7200053	0.93[ASN][1000 genomes]
rs7202596	0.97[ASN][1000 genomes]
rs7204984	0.93[ASN][1000 genomes]
rs7206665	0.93[ASN][1000 genomes]
rs8055490	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055974	0.81[ASN][1000 genomes]
rs8056141	0.83[ASN][1000 genomes]
rs8057084	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8063068	0.96[ASN][1000 genomes]
rs977985	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977986	0.81[ASN][1000 genomes]
rs977987	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9923834	0.81[ASN][1000 genomes]
rs9933255	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	esv3485939	chr16:75497453-75550284	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3485940	chr16:75497453-75550284	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62060550	RP11-252K23.2	cis	Thyroid	GTEx
rs62060550	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs62060550	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs62060550	RP11-252K23.2	cis	lung	GTEx
rs62060550	RP11-252K23.2	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75498600-75506800	Weak transcription	Brain Substantia Nigra	brain
2	chr16:75498600-75511800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:75498800-75504000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr16:75498800-75505200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:75498800-75505600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr16:75498800-75505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:75498800-75507200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:75498800-75518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:75499000-75511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr16:75499000-75511200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:75499000-75511200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr16:75499200-75502400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr16:75499200-75505800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:75499200-75505800	Weak transcription	Fetal Heart	heart
15	chr16:75499200-75506000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:75499200-75506200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr16:75499200-75511400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:75499200-75511400	Weak transcription	Brain Anterior Caudate	brain
19	chr16:75499200-75519600	Weak transcription	Fetal Intestine Small	intestine
20	chr16:75499400-75505600	Weak transcription	Hela-S3	cervix
21	chr16:75501400-75506000	Weak transcription	HepG2	liver
22	chr16:75501600-75504200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr16:75502200-75502400	Enhancers	Monocytes-CD14+_RO01746	blood

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