Variant report

Variant	rs11209938
Chromosome Location	chr1:72697178-72697179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10493494	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209923	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11209928	0.83[ASN][1000 genomes]
rs11209932	0.82[ASN][1000 genomes]
rs11209933	0.82[ASN][1000 genomes]
rs11209935	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583451	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11587829	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11587895	0.86[ASN][1000 genomes]
rs1194265	0.90[ASN][1000 genomes]
rs1194267	0.90[ASN][1000 genomes]
rs1194269	0.90[ASN][1000 genomes]
rs1194270	0.84[ASN][1000 genomes]
rs1194271	0.90[ASN][1000 genomes]
rs1194273	0.90[ASN][1000 genomes]
rs1194277	0.90[ASN][1000 genomes]
rs1194278	0.88[ASN][1000 genomes]
rs1194281	0.86[ASN][1000 genomes]
rs1194282	0.90[ASN][1000 genomes]
rs1194283	0.90[ASN][1000 genomes]
rs1194284	0.90[ASN][1000 genomes]
rs1194286	0.90[ASN][1000 genomes]
rs12036585	0.81[ASN][1000 genomes]
rs1205484	0.90[ASN][1000 genomes]
rs1209251	0.90[ASN][1000 genomes]
rs12124902	0.81[AMR][1000 genomes]
rs12125336	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136617	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12137663	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12139652	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12141242	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1342863	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1342874	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1385920	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1385921	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1486097	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1486111	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1675356	0.86[ASN][1000 genomes]
rs17524209	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17525406	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589316	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1858600	0.88[ASN][1000 genomes]
rs2066416	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126077	0.90[ASN][1000 genomes]
rs2153929	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298151	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298152	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2630431	0.82[ASN][1000 genomes]
rs2797540	0.89[ASN][1000 genomes]
rs2797543	0.90[ASN][1000 genomes]
rs2821285	0.87[ASN][1000 genomes]
rs2821288	0.87[ASN][1000 genomes]
rs2821296	0.82[ASN][1000 genomes]
rs55777234	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6656980	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659016	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668604	0.82[ASN][1000 genomes]
rs6698979	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6699841	0.82[ASN][1000 genomes]
rs7349073	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517387	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7518919	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529364	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7549778	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs985227	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv461939	chr1:72555489-72717743	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546482	chr1:72555489-72717743	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1013250	chr1:72603540-72762582	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv830192	chr1:72616562-72806118	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv461951	chr1:72634912-72707226	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
11	nsv546485	chr1:72634912-72707226	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
12	nsv1014832	chr1:72642420-72823477	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv534997	chr1:72642420-72823477	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv546486	chr1:72654730-72729142	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72692200-72698800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:72694200-72698200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:72695400-72697200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:72695600-72697200	Enhancers	NHDF-Ad	bronchial
5	chr1:72695800-72697200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:72695800-72698200	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:72695800-72698200	Weak transcription	HepG2	liver
8	chr1:72696000-72697200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:72696200-72697200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:72697000-72698200	Weak transcription	Rectal Smooth Muscle	rectum

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