Variant report

Variant	rs877776
Chromosome Location	chr1:152178018-152178019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCE5A-3	chr1:152177537-152178552	NONHSAT006473

Extended variants
information (count: 142 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10749668	0.88[ASW][hapmap]
rs10749669	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10749670	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10788824	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10788826	0.94[ASW][hapmap]
rs10788827	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10788828	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10888466	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10888467	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888470	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];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10888471	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888473	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];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10888475	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204933	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204937	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204938	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204939	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204944	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11204947	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11204948	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11204949	0.84[GIH][hapmap]
rs11204951	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204952	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204978	0.91[CEU][hapmap]
rs11204980	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11204981	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11583524	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11584340	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11584427	0.92[CEU][hapmap]
rs11586114	0.93[CEU][hapmap]
rs11587676	0.93[CEU][hapmap]
rs11588174	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589532	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589587	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12047544	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12063165	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12116736	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12117911	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12144058	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12405278	0.84[CHD][hapmap]
rs12405678	0.82[AMR][1000 genomes]
rs12408581	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12409762	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567463	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12748016	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12749966	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12754479	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1353436	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1390485	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1390487	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1390488	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]
rs1390490	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs1466757	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1496045	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs1496049	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1496050	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1496051	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1552992	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552993	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552996	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1845791	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1858480	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1858482	0.93[CEU][hapmap]
rs1969019	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2065955	0.93[CEU][hapmap]
rs2132418	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2184953	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2291770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338430	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2338431	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2338432	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2338555	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2879174	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3120659	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs3126066	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3126085	0.86[CEU][hapmap];0.95[CHD][hapmap]
rs3126088	0.93[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap]
rs3126091	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs36033453	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41266134	0.82[AMR][1000 genomes]
rs4326625	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4379679	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4415568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4456098	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4511113	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4514243	0.90[ASN][1000 genomes]
rs4845421	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845423	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs4845426	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845428	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845430	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4845431	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4845733	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845734	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845736	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845737	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4845740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845741	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845743	0.82[ASN][1000 genomes]
rs4845744	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845745	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845750	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845751	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845752	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55982921	0.82[EUR][1000 genomes]
rs56013982	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56407906	0.83[ASN][1000 genomes]
rs6587647	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587651	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587652	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587666	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6662450	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666382	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6675889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6676012	0.85[AMR][1000 genomes]
rs6678951	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72696963	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72696969	0.82[AMR][1000 genomes]
rs74127901	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7520249	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7531094	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533529	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534716	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7535078	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7535536	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7537637	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7550106	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs868303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs868304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs991231	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	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
7	esv1795677	chr1:152175970-152183601	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv946314	chr1:152177841-152178916	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs877776	FLG-AS1	cis	Thyroid	GTEx
rs877776	JTB	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152162200-152180200	Weak transcription	Ovary	ovary
2	chr1:152164400-152178400	Weak transcription	Esophagus	oesophagus
3	chr1:152173000-152180200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:152178000-152180000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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