Variant report

Variant	rs1669410
Chromosome Location	chr12:11338559-11338560
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	chr12:11331591..11333492-chr12:11338114..11339808,2	K562	blood:
2	chr12:11328652..11331846-chr12:11337152..11339281,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256629	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs11557132	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376742	0.83[ASN][1000 genomes]
rs1451765	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451766	0.82[ASN][1000 genomes]
rs1451772	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451774	0.82[ASN][1000 genomes]
rs1551191	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1551192	0.83[ASN][1000 genomes]
rs1650020	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1650029	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1650030	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1650031	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1650053	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669412	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669414	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669418	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669422	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17817150	0.82[ASN][1000 genomes]
rs1817104	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1823663	0.83[ASN][1000 genomes]
rs1823664	0.83[ASN][1000 genomes]
rs1839859	0.83[ASN][1000 genomes]
rs2008253	0.83[ASN][1000 genomes]
rs2019629	0.83[ASN][1000 genomes]
rs2019633	0.83[ASN][1000 genomes]
rs2123006	0.95[ASN][1000 genomes]
rs2123007	0.95[ASN][1000 genomes]
rs2167481	0.95[ASN][1000 genomes]
rs2218818	0.82[ASN][1000 genomes]
rs2416544	0.95[ASN][1000 genomes]
rs2416545	0.95[ASN][1000 genomes]
rs2416546	0.95[ASN][1000 genomes]
rs2416547	0.95[ASN][1000 genomes]
rs2559581	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2597918	0.82[ASN][1000 genomes]
rs2597919	0.83[ASN][1000 genomes]
rs2597920	0.83[ASN][1000 genomes]
rs2597921	0.83[ASN][1000 genomes]
rs2597923	0.83[ASN][1000 genomes]
rs2599396	0.83[ASN][1000 genomes]
rs2599404	0.83[ASN][1000 genomes]
rs2600350	0.82[ASN][1000 genomes]
rs2600351	0.83[ASN][1000 genomes]
rs2600352	0.83[ASN][1000 genomes]
rs2600353	0.83[ASN][1000 genomes]
rs2600354	0.83[ASN][1000 genomes]
rs2600357	0.83[ASN][1000 genomes]
rs2708331	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708368	0.82[ASN][1000 genomes]
rs2708369	0.82[ASN][1000 genomes]
rs2708370	0.83[ASN][1000 genomes]
rs2923860	0.83[ASN][1000 genomes]
rs319267	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs319268	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs319271	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs319272	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs319273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319274	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34000114	0.82[ASN][1000 genomes]
rs34018339	0.95[ASN][1000 genomes]
rs34082341	0.83[ASN][1000 genomes]
rs34134804	0.82[ASN][1000 genomes]
rs34241192	0.83[ASN][1000 genomes]
rs34270405	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34272839	0.82[ASN][1000 genomes]
rs34288418	0.83[ASN][1000 genomes]
rs34327967	0.83[ASN][1000 genomes]
rs34436598	0.83[ASN][1000 genomes]
rs34531956	0.95[ASN][1000 genomes]
rs34536990	0.83[ASN][1000 genomes]
rs34548551	0.83[ASN][1000 genomes]
rs34590962	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34648613	0.82[ASN][1000 genomes]
rs34685506	0.83[ASN][1000 genomes]
rs34769150	0.83[ASN][1000 genomes]
rs34843817	0.83[ASN][1000 genomes]
rs34927715	0.83[ASN][1000 genomes]
rs34949195	0.82[ASN][1000 genomes]
rs35017789	0.82[ASN][1000 genomes]
rs35021653	0.83[ASN][1000 genomes]
rs35119575	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35124606	0.83[ASN][1000 genomes]
rs35151793	0.95[ASN][1000 genomes]
rs35183723	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35280352	0.83[ASN][1000 genomes]
rs35340812	0.83[ASN][1000 genomes]
rs35499317	0.82[ASN][1000 genomes]
rs35650731	0.82[ASN][1000 genomes]
rs35699328	0.83[ASN][1000 genomes]
rs35813024	0.83[ASN][1000 genomes]
rs35856529	0.83[ASN][1000 genomes]
rs35893804	0.83[ASN][1000 genomes]
rs35969491	0.82[ASN][1000 genomes]
rs36050405	0.83[ASN][1000 genomes]
rs36062343	0.83[ASN][1000 genomes]
rs36115011	0.83[ASN][1000 genomes]
rs3863325	0.82[ASN][1000 genomes]
rs3906996	0.83[ASN][1000 genomes]
rs3911234	0.82[ASN][1000 genomes]
rs3911800	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4101885	0.82[ASN][1000 genomes]
rs4763638	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5020531	0.82[ASN][1000 genomes]
rs61928449	0.82[ASN][1000 genomes]
rs61928562	0.83[ASN][1000 genomes]
rs61928564	0.83[ASN][1000 genomes]
rs61928565	0.83[ASN][1000 genomes]
rs61928566	0.83[ASN][1000 genomes]
rs61928569	0.83[ASN][1000 genomes]
rs61928595	0.83[ASN][1000 genomes]
rs61928597	0.83[ASN][1000 genomes]
rs61928602	0.83[ASN][1000 genomes]
rs61928610	0.83[ASN][1000 genomes]
rs61928618	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61928619	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61928642	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61928643	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61928644	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61928646	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61931266	0.82[ASN][1000 genomes]
rs61931270	0.83[ASN][1000 genomes]
rs61931274	0.83[ASN][1000 genomes]
rs61931278	0.80[ASN][1000 genomes]
rs61931279	0.82[ASN][1000 genomes]
rs6488347	0.84[ASN][1000 genomes]
rs6488348	0.84[ASN][1000 genomes]
rs6488349	0.84[ASN][1000 genomes]
rs6488350	0.84[ASN][1000 genomes]
rs6488351	0.83[ASN][1000 genomes]
rs6488355	0.83[ASN][1000 genomes]
rs6488356	0.83[ASN][1000 genomes]
rs6488357	0.82[ASN][1000 genomes]
rs6488358	0.82[ASN][1000 genomes]
rs67471783	0.82[ASN][1000 genomes]
rs67955183	0.82[ASN][1000 genomes]
rs7132674	0.82[ASN][1000 genomes]
rs7136602	0.82[ASN][1000 genomes]
rs71453440	0.82[ASN][1000 genomes]
rs7298544	0.82[ASN][1000 genomes]
rs7302010	0.83[ASN][1000 genomes]
rs7302711	0.82[ASN][1000 genomes]
rs7310047	0.83[ASN][1000 genomes]
rs7313796	0.83[ASN][1000 genomes]
rs7486717	0.83[ASN][1000 genomes]
rs7955495	0.83[ASN][1000 genomes]
rs7959320	0.83[ASN][1000 genomes]
rs7960823	0.83[ASN][1000 genomes]
rs7965506	0.83[ASN][1000 genomes]
rs7969625	0.95[ASN][1000 genomes]
rs7970225	0.81[ASN][1000 genomes]
rs7973730	0.83[ASN][1000 genomes]
rs7976211	0.83[ASN][1000 genomes]
rs7976950	0.82[ASN][1000 genomes]
rs8300	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs977473	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' 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	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv8918	chr12:11337700-11339877	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1669410	PRR4	cis	lung	GTEx
rs1669410	RP11-434C1.1	cis	lung	GTEx
rs1669410	PRR4	cis	Nerve Tibial	GTEx
rs1669410	PRR4	cis	Muscle Skeletal	GTEx
rs1669410	PRR4	cis	Thyroid	GTEx
rs1669410	PRR4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11326200-11338600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr12:11326400-11355600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:11328000-11338600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:11328800-11340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:11330600-11365400	Weak transcription	Primary T cells from cord blood	blood

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