Variant report

Variant	rs1390488
Chromosome Location	chr1:152199500-152199501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152161770..152163117-chr1:152199462..152200464,10	MCF-7	breast:
2	chr1:152160950..152161743-chr1:152199424..152200319,5	MCF-7	breast:
3	chr1:152160624..152161417-chr1:152199475..152200038,4	MCF-7	breast:
4	chr1:152161230..152163433-chr1:152198325..152200972,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237975	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10749669	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10749670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788824	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];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	0.85[ASN][1000 genomes]
rs10888466	0.86[EUR][1000 genomes]
rs10888467	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10888468	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10888470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888475	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888476	0.88[ASN][1000 genomes]
rs10888477	0.84[ASN][1000 genomes]
rs10888478	0.85[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]
rs11204939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204944	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204945	0.82[ASN][1000 genomes]
rs11204947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204949	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11204951	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204952	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204976	0.80[ASN][1000 genomes]
rs11204978	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs11204980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11204981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs11583524	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11584340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11584427	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs11586114	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs11587676	0.93[CEU][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs11588174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11589532	0.91[EUR][1000 genomes]
rs12027899	0.82[ASN][1000 genomes]
rs12032307	0.81[ASN][1000 genomes]
rs12045492	0.82[ASN][1000 genomes]
rs12045496	0.82[ASN][1000 genomes]
rs12047544	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12063165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12065368	0.81[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]
rs12405278	0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap]
rs12405678	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12409762	0.91[EUR][1000 genomes]
rs12409802	0.86[ASN][1000 genomes]
rs12567463	0.90[EUR][1000 genomes]
rs12730241	0.80[ASN][1000 genomes]
rs12748016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.94[ASN][1000 genomes]
rs1390490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1466757	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1496045	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
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];0.80[ASN][1000 genomes]
rs1552993	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1552995	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1552996	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1845791	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1858482	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs1969019	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065955	0.93[CEU][hapmap]
rs2132418	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2184950	0.80[ASN][1000 genomes]
rs2184951	0.80[ASN][1000 genomes]
rs2184953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2291770	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2338430	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338431	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2338432	0.80[AMR][1000 genomes]
rs2338555	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2879174	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs3126062	0.80[ASN][1000 genomes]
rs3126066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3126085	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs3126088	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap]
rs3126091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs36033453	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41266134	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4256811	0.85[ASN][1000 genomes]
rs4326625	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4341364	0.85[ASN][1000 genomes]
rs4361987	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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];0.92[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	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845421	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845423	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4845426	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845428	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845430	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845431	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845733	0.86[EUR][1000 genomes]
rs4845734	0.88[EUR][1000 genomes]
rs4845736	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845737	0.91[JPT][hapmap]
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	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845751	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845752	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845753	0.84[ASN][1000 genomes]
rs55957623	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6587647	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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];0.95[ASN][1000 genomes]
rs6587666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6662450	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6666382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670891	0.86[ASN][1000 genomes]
rs6675889	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6676012	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678951	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6692010	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72696969	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74127901	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535078	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	0.83[ASN][1000 genomes]
rs7537637	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540844	0.88[ASN][1000 genomes]
rs7543541	0.88[ASN][1000 genomes]
rs7550106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs991231	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	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	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1390488	FLG-AS1	cis	Thyroid	GTEx
rs1390488	JTB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152197800-152200000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152197800-152200200	Enhancers	HMEC	breast
3	chr1:152197800-152200200	Enhancers	NHEK	skin
4	chr1:152198600-152201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:152199400-152200600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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