Variant report

Variant	rs6040669
Chromosome Location	chr20:11412024-11412025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009747	0.82[ASN][1000 genomes]
rs1009748	0.82[ASN][1000 genomes]
rs10485748	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11696745	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11696986	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11698313	0.83[ASN][1000 genomes]
rs11699470	0.84[ASN][1000 genomes]
rs11699490	0.83[ASN][1000 genomes]
rs13038146	0.84[ASN][1000 genomes]
rs17189710	0.84[ASN][1000 genomes]
rs17261909	0.84[ASN][1000 genomes]
rs2207116	0.82[ASN][1000 genomes]
rs2207117	0.81[ASN][1000 genomes]
rs2327412	0.83[ASN][1000 genomes]
rs2876227	0.85[ASN][1000 genomes]
rs4270409	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4315598	0.83[ASN][1000 genomes]
rs4444612	0.83[ASN][1000 genomes]
rs4813995	0.83[ASN][1000 genomes]
rs4814001	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4814018	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55970622	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56383233	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033135	0.82[ASN][1000 genomes]
rs6033137	0.83[ASN][1000 genomes]
rs6033138	0.83[ASN][1000 genomes]
rs6040633	0.82[ASN][1000 genomes]
rs6040636	0.82[ASN][1000 genomes]
rs6040637	0.82[ASN][1000 genomes]
rs6040638	0.82[ASN][1000 genomes]
rs6040644	0.83[ASN][1000 genomes]
rs6040646	0.83[ASN][1000 genomes]
rs6040647	0.83[ASN][1000 genomes]
rs6040648	0.83[ASN][1000 genomes]
rs6040649	0.83[ASN][1000 genomes]
rs6040657	0.84[ASN][1000 genomes]
rs6040660	0.84[ASN][1000 genomes]
rs6040661	0.84[ASN][1000 genomes]
rs6040663	0.83[ASN][1000 genomes]
rs6040665	0.83[ASN][1000 genomes]
rs6040666	0.84[ASN][1000 genomes]
rs6040668	0.83[ASN][1000 genomes]
rs6040759	0.85[CEU][hapmap]
rs6131203	0.82[ASN][1000 genomes]
rs6131206	0.84[ASN][1000 genomes]
rs6131208	0.84[ASN][1000 genomes]
rs6134243	0.82[ASN][1000 genomes]
rs62191897	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62191904	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62191905	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62191909	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62191910	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62191911	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079893	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs742827	0.83[ASN][1000 genomes]
rs8125140	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs926909	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs973969	0.87[AMR][1000 genomes];0.89[EUR][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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432099	chr20:11371093-11476900	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1058734	chr20:11389232-11479953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv522929	chr20:11411026-11516418	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11408000-11415000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr20:11410200-11413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:11410200-11413000	Weak transcription	HMEC	breast
4	chr20:11410200-11413000	Weak transcription	NHEK	skin
5	chr20:11410400-11413000	Weak transcription	A549	lung
6	chr20:11410600-11413000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:11410800-11412600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr20:11411400-11414200	Weak transcription	Psoas Muscle	Psoas
9	chr20:11411600-11413600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:11411800-11415600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:11412000-11413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:11412000-11413600	Enhancers	Osteobl	bone
13	chr20:11412000-11416400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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