Variant report

Variant	rs11204939
Chromosome Location	chr1:152200942-152200943
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152161796..152162773-chr1:152200555..152201151,2	MCF-7	breast:
2	chr1:152161230..152163433-chr1:152198325..152200972,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237975	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10749669	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10749670	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788824	0.81[EUR][1000 genomes]
rs10788827	0.82[AMR][1000 genomes]
rs10788828	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788831	0.86[ASN][1000 genomes]
rs10888466	0.86[EUR][1000 genomes]
rs10888467	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10888468	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10888470	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888473	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888475	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888476	0.88[ASN][1000 genomes]
rs10888477	0.85[ASN][1000 genomes]
rs10888478	0.86[ASN][1000 genomes]
rs11204933	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204937	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204944	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204945	0.81[ASN][1000 genomes]
rs11204947	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204948	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204949	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11204951	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204952	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583524	0.81[EUR][1000 genomes]
rs11588174	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11589532	0.91[EUR][1000 genomes]
rs12027899	0.81[ASN][1000 genomes]
rs12032307	0.81[ASN][1000 genomes]
rs12045492	0.81[ASN][1000 genomes]
rs12045496	0.81[ASN][1000 genomes]
rs12047544	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12063165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12065368	0.80[ASN][1000 genomes]
rs12117911	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12144058	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12405678	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12409762	0.91[EUR][1000 genomes]
rs12409802	0.86[ASN][1000 genomes]
rs12567463	0.90[EUR][1000 genomes]
rs12748016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749966	0.85[EUR][1000 genomes]
rs12754479	0.82[AMR][1000 genomes]
rs1353436	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1390485	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1390487	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1390488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466757	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1496049	0.82[EUR][1000 genomes]
rs1496050	0.86[EUR][1000 genomes]
rs1496051	0.86[EUR][1000 genomes]
rs1552992	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1552993	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1552995	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1552996	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1845791	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1969019	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132418	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291770	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2338430	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2338431	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2338432	0.80[AMR][1000 genomes]
rs2879174	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36033453	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41266134	0.81[AMR][1000 genomes]
rs4256811	0.86[ASN][1000 genomes]
rs4326625	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4341364	0.86[ASN][1000 genomes]
rs4361987	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4415568	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4421596	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4456097	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4456098	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4466659	0.84[ASN][1000 genomes]
rs4511111	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4511113	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845421	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845426	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845428	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845430	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845431	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845733	0.86[EUR][1000 genomes]
rs4845734	0.88[EUR][1000 genomes]
rs4845736	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845740	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845741	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845742	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845744	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845745	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845751	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845752	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845753	0.85[ASN][1000 genomes]
rs55957623	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6587647	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587651	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587652	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662450	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666382	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670891	0.86[ASN][1000 genomes]
rs6675889	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676012	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678951	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692010	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72696969	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74127901	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520249	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7531094	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7533529	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7534716	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535078	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535536	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536879	0.84[ASN][1000 genomes]
rs7537637	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7540844	0.88[ASN][1000 genomes]
rs7543541	0.88[ASN][1000 genomes]
rs7550106	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868303	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs868304	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs877776	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs991231	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11204939	FLG-AS1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152198600-152201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:152200000-152201000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152200600-152201800	Enhancers	HMEC	breast
4	chr1:152200600-152202200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152200600-152202200	Enhancers	NHEK	skin

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