Variant report

Variant	rs7540844
Chromosome Location	chr1:152230586-152230587
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10749670	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788828	0.83[ASN][1000 genomes]
rs10788831	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888470	0.88[ASN][1000 genomes]
rs10888471	0.88[ASN][1000 genomes]
rs10888473	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10888475	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888476	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888477	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204937	0.81[ASN][1000 genomes]
rs11204938	0.81[ASN][1000 genomes]
rs11204939	0.88[ASN][1000 genomes]
rs11204944	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204947	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204948	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204951	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204952	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204956	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204976	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204980	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204981	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11485508	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576858	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11584340	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12027807	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12027899	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12045492	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12045496	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065368	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12406105	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407553	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409802	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12730241	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12748016	0.86[ASN][1000 genomes]
rs1390487	0.82[ASN][1000 genomes]
rs1390488	0.88[ASN][1000 genomes]
rs1466757	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1845791	0.92[ASN][1000 genomes]
rs1858479	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1858480	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969019	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132418	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184950	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2184951	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2184953	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338430	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2879174	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3120642	0.83[EUR][1000 genomes]
rs3120653	0.82[EUR][1000 genomes]
rs3120659	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3120661	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126055	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3126056	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3126058	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3126060	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3126062	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3126066	0.82[ASN][1000 genomes]
rs3126067	0.82[ASN][1000 genomes]
rs3126072	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3126074	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3126079	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3126091	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126094	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126097	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34188926	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36033453	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41267154	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4256811	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4326625	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4341364	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4361987	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4456097	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4466659	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4511113	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845426	0.83[ASN][1000 genomes]
rs4845428	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845430	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845431	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845750	0.88[ASN][1000 genomes]
rs4845751	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845752	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845753	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55650366	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55654502	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57672167	0.82[EUR][1000 genomes]
rs6587647	0.84[ASN][1000 genomes]
rs6587651	0.81[ASN][1000 genomes]
rs6587652	0.84[ASN][1000 genomes]
rs6587666	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6666382	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6670891	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6675889	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678951	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681433	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681457	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6692010	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71625201	0.80[EUR][1000 genomes]
rs72697000	0.85[ASN][1000 genomes]
rs74127901	0.86[ASN][1000 genomes]
rs74129461	0.82[EUR][1000 genomes]
rs7520249	0.83[ASN][1000 genomes]
rs7534716	0.88[ASN][1000 genomes]
rs7535078	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7535536	0.81[ASN][1000 genomes]
rs7536879	0.86[ASN][1000 genomes]
rs7537637	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550106	0.83[ASN][1000 genomes]
rs9435974	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9436062	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs991231	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv946325	chr1:152221751-152240196	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152225400-152232200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152225600-152232200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152229600-152230800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr1:152230200-152230600	ZNF genes & repeats	Aorta	Aorta
5	chr1:152230200-152230600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr1:152230200-152230600	ZNF genes & repeats	Fetal Stomach	stomach
7	chr1:152230200-152230600	ZNF genes & repeats	Left Ventricle	heart
8	chr1:152230200-152230600	ZNF genes & repeats	Ovary	ovary
9	chr1:152230200-152230600	ZNF genes & repeats	Psoas Muscle	Psoas
10	chr1:152230200-152230800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:152230200-152230800	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr1:152230200-152230800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
13	chr1:152230400-152230600	ZNF genes & repeats	Brain Angular Gyrus	brain
14	chr1:152230400-152230600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
15	chr1:152230400-152231200	ZNF genes & repeats	Fetal Kidney	kidney
16	chr1:152230400-152235800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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