Variant report

Variant	rs1778205
Chromosome Location	chr1:95052228-95052229
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-F3-1	chr1:95051112-95052318	XLOC_000921

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1041041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1041042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146476	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146477	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146480	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146481	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146482	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146484	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1146485	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146487	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146489	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146491	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146492	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1146494	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1146496	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146498	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146500	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1146501	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11485356	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12075529	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12354005	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1245215	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1303132	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1303134	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1303135	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303137	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1303138	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1303139	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1324217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1408341	0.88[ASN][1000 genomes]
rs1578535	0.86[ASN][1000 genomes]
rs1612481	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1772904	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1772911	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1778206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778207	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778223	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1778226	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2093843	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2762509	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2794475	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2794476	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2794479	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2971946	0.83[ASN][1000 genomes]
rs2971947	0.85[ASN][1000 genomes]
rs2985287	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2996292	0.82[ASN][1000 genomes]
rs6668501	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68169338	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs927633	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs927634	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs927635	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927636	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs968661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs968662	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1804937	chr1:95051930-95081587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region 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	chr1:95046000-95065400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:95046400-95055200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:95047000-95055800	Weak transcription	NHLF	lung
4	chr1:95051600-95052600	Enhancers	Dnd41	blood
5	chr1:95051800-95052400	Enhancers	HSMM	muscle
6	chr1:95052000-95052400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:95052200-95052400	Enhancers	Brain Germinal Matrix	brain
8	chr1:95052200-95053000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links