Variant report

Variant	rs3001406
Chromosome Location	chr1:73364782-73364783
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEGR1-1	chr1:73364712-73364823	ENSG00000225087

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10890001	0.90[ASN][1000 genomes]
rs10890002	0.86[ASN][1000 genomes]
rs11210090	1.00[ASN][1000 genomes]
rs11210093	0.98[ASN][1000 genomes]
rs11210116	0.90[ASN][1000 genomes]
rs12041212	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1358033	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17093667	0.94[ASN][1000 genomes]
rs2177839	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692843	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692845	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692849	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4292906	1.00[ASN][1000 genomes]
rs4342807	0.98[ASN][1000 genomes]
rs4344271	0.94[ASN][1000 genomes]
rs4396073	0.90[ASN][1000 genomes]
rs4592216	0.81[ASN][1000 genomes]
rs4649970	1.00[ASN][1000 genomes]
rs55693193	0.83[ASN][1000 genomes]
rs55710119	0.86[ASN][1000 genomes]
rs55711267	0.90[ASN][1000 genomes]
rs55871113	0.88[ASN][1000 genomes]
rs56073791	0.90[ASN][1000 genomes]
rs56355427	0.86[ASN][1000 genomes]
rs56681081	0.86[ASN][1000 genomes]
rs56742425	0.86[ASN][1000 genomes]
rs56996808	0.86[ASN][1000 genomes]
rs57118574	0.86[ASN][1000 genomes]
rs57135981	0.90[ASN][1000 genomes]
rs57345656	0.86[ASN][1000 genomes]
rs57458135	0.90[ASN][1000 genomes]
rs58252227	0.86[ASN][1000 genomes]
rs58687178	0.86[ASN][1000 genomes]
rs58759875	0.86[ASN][1000 genomes]
rs58801081	0.86[ASN][1000 genomes]
rs59074407	0.86[ASN][1000 genomes]
rs59291669	0.90[ASN][1000 genomes]
rs59381674	0.84[ASN][1000 genomes]
rs59663011	0.94[ASN][1000 genomes]
rs59674856	0.86[ASN][1000 genomes]
rs60001238	0.90[ASN][1000 genomes]
rs60262946	0.86[ASN][1000 genomes]
rs60357441	0.86[ASN][1000 genomes]
rs60453462	0.86[ASN][1000 genomes]
rs60711999	0.88[ASN][1000 genomes]
rs60715960	0.86[ASN][1000 genomes]
rs60921218	0.88[ASN][1000 genomes]
rs61003856	0.90[ASN][1000 genomes]
rs61022613	0.86[ASN][1000 genomes]
rs61027335	0.94[ASN][1000 genomes]
rs61029701	0.86[ASN][1000 genomes]
rs61071256	0.86[ASN][1000 genomes]
rs61094497	0.86[ASN][1000 genomes]
rs61229063	0.86[ASN][1000 genomes]
rs61464284	0.86[ASN][1000 genomes]
rs6692856	1.00[ASN][1000 genomes]
rs74090509	0.90[ASN][1000 genomes]
rs74090513	0.90[ASN][1000 genomes]
rs74090514	0.90[ASN][1000 genomes]
rs74090526	0.90[ASN][1000 genomes]
rs74090527	0.90[ASN][1000 genomes]
rs74090532	0.90[ASN][1000 genomes]
rs74090533	0.90[ASN][1000 genomes]
rs74090534	0.90[ASN][1000 genomes]
rs74090535	0.94[ASN][1000 genomes]
rs74090538	0.94[ASN][1000 genomes]
rs74090540	0.94[ASN][1000 genomes]
rs74090541	0.94[ASN][1000 genomes]
rs74090543	0.94[ASN][1000 genomes]
rs74090546	0.90[ASN][1000 genomes]
rs74090547	0.90[ASN][1000 genomes]
rs74090550	0.90[ASN][1000 genomes]
rs74090553	0.84[ASN][1000 genomes]
rs74090555	0.90[ASN][1000 genomes]
rs74090556	0.90[ASN][1000 genomes]
rs74090557	0.90[ASN][1000 genomes]
rs74090559	0.90[ASN][1000 genomes]
rs74091214	0.86[ASN][1000 genomes]
rs74091215	0.86[ASN][1000 genomes]
rs74091216	0.86[ASN][1000 genomes]
rs74091260	0.86[ASN][1000 genomes]
rs74091266	0.86[ASN][1000 genomes]
rs74091268	0.86[ASN][1000 genomes]
rs74091272	0.86[ASN][1000 genomes]
rs74091275	0.86[ASN][1000 genomes]
rs74091277	0.86[ASN][1000 genomes]
rs74091279	0.86[ASN][1000 genomes]
rs74091280	0.86[ASN][1000 genomes]
rs74091281	0.86[ASN][1000 genomes]
rs74091283	0.86[ASN][1000 genomes]
rs74091287	0.86[ASN][1000 genomes]
rs74091288	0.86[ASN][1000 genomes]
rs74091291	0.86[ASN][1000 genomes]
rs74091295	0.86[ASN][1000 genomes]
rs74091297	0.86[ASN][1000 genomes]
rs74092376	0.88[ASN][1000 genomes]
rs74092377	0.86[ASN][1000 genomes]
rs74092379	0.88[ASN][1000 genomes]
rs74092380	0.88[ASN][1000 genomes]
rs74092381	0.88[ASN][1000 genomes]
rs74092384	0.88[ASN][1000 genomes]
rs74092388	0.88[ASN][1000 genomes]
rs74092389	0.86[ASN][1000 genomes]
rs74092392	0.86[ASN][1000 genomes]
rs74092393	0.86[ASN][1000 genomes]
rs74092394	0.86[ASN][1000 genomes]
rs74092400	0.86[ASN][1000 genomes]
rs74092402	0.86[ASN][1000 genomes]
rs74092628	0.90[ASN][1000 genomes]
rs74092629	0.90[ASN][1000 genomes]
rs74092630	0.90[ASN][1000 genomes]
rs74092631	0.90[ASN][1000 genomes]
rs74092632	0.90[ASN][1000 genomes]
rs74092633	0.90[ASN][1000 genomes]
rs74092634	0.90[ASN][1000 genomes]
rs74092637	0.88[ASN][1000 genomes]
rs74094603	0.86[ASN][1000 genomes]
rs74094604	0.86[ASN][1000 genomes]
rs74094606	0.86[ASN][1000 genomes]
rs7412164	0.86[ASN][1000 genomes]
rs7412167	0.80[ASN][1000 genomes]
rs7511969	0.90[ASN][1000 genomes]
rs7519779	0.90[ASN][1000 genomes]
rs7519879	0.90[ASN][1000 genomes]
rs7529186	0.88[ASN][1000 genomes]
rs7535137	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542800	0.90[ASN][1000 genomes]
rs9425114	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661859	0.98[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	nsv1013549	chr1:73209040-73408373	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012319	chr1:73337418-73547086	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3413041	chr1:73363980-73381345	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:73362800-73365000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:73363000-73365000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:73364000-73364800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:73364000-73365000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:73364000-73365000	Active TSS	Hela-S3	cervix
6	chr1:73364200-73365000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr1:73364400-73365000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:73364600-73365000	Active TSS	H9 Cell Line	embryonic stem cell

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