Variant report

Variant	rs9543972
Chromosome Location	chr13:76121675-76121676
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	chr13:76109687..76114004-chr13:76118514..76122227,3	K562	blood:

Variant related genes	Relation type
ENSG00000188243	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12427755	0.87[ASN][1000 genomes]
rs12427931	0.87[ASN][1000 genomes]
rs12428989	0.87[ASN][1000 genomes]
rs1535724	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031236	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296146	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328959	0.89[ASN][1000 genomes]
rs2328960	0.93[ASN][1000 genomes]
rs2328963	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2328964	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876706	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3783028	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3818355	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4611344	0.95[ASN][1000 genomes]
rs4885318	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4885322	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4885323	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4885324	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55777620	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55927305	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6562913	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6562914	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6562915	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6562916	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6562918	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7139740	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7317250	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73223968	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73223984	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324195	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7329512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7339146	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7981698	0.87[ASN][1000 genomes]
rs7982517	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7986566	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7989568	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7996884	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8192755	0.95[ASN][1000 genomes]
rs8192756	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8192762	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8192763	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8192764	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9318361	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9530447	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9543976	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9543990	0.95[ASN][1000 genomes]
rs9543992	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9544004	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9565177	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9573591	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9573592	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs974373	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv900565	chr13:76111280-76169347	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9543972	RP11-173B14.5	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76112200-76123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:76112600-76122800	Weak transcription	Fetal Brain Male	brain
3	chr13:76112600-76123000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:76112600-76123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76112600-76123600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:76112800-76122800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:76112800-76122800	Weak transcription	Brain Anterior Caudate	brain
8	chr13:76112800-76123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:76112800-76123000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:76112800-76123000	Weak transcription	Adipose Nuclei	Adipose
11	chr13:76116000-76123000	Weak transcription	GM12878-XiMat	blood
12	chr13:76116400-76123200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:76119400-76123000	Weak transcription	Fetal Kidney	kidney
14	chr13:76119400-76123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:76119600-76121800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:76119600-76121800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:76119600-76121800	Weak transcription	HepG2	liver
18	chr13:76119600-76121800	Weak transcription	Osteobl	bone
19	chr13:76119600-76123000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:76119600-76123000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:76119600-76123000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:76119600-76123000	Weak transcription	Liver	Liver
23	chr13:76119600-76123000	Weak transcription	Hela-S3	cervix
24	chr13:76119600-76123000	Weak transcription	HMEC	breast
25	chr13:76119600-76123000	Weak transcription	NHDF-Ad	bronchial
26	chr13:76119600-76123000	Weak transcription	NHEK	skin
27	chr13:76119600-76123200	Weak transcription	NHLF	lung
28	chr13:76119800-76122200	Weak transcription	K562	blood
29	chr13:76120000-76121800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr13:76120000-76123000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:76120000-76123000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:76120000-76123000	Weak transcription	Psoas Muscle	Psoas
33	chr13:76120000-76123200	Weak transcription	Placenta	Placenta
34	chr13:76120600-76123000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:76120800-76123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:76121000-76123000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:76121200-76123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:76121600-76123200	Enhancers	Rectal Mucosa Donor 31	rectum

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