Variant report

Variant	rs1883956
Chromosome Location	chr20:22997466-22997467
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THBD-1	chr20:22997393-22997495	XLOC_013687
2	lnc-THBD-1	chr20:22997393-22997495	ENSG00000230492.1
3	lnc-THBD-1	chr20:22997393-22997495	NONHSAT079018
4	lnc-THBD-1	chr20:22997393-22997495	NONHSAT079019

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10485639	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13036275	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13042418	0.90[EUR][1000 genomes]
rs1331071	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207106	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2207107	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2268199	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34112928	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34217171	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34854430	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34980833	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35745073	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36016048	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3746726	0.81[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3746728	0.91[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6076008	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6076009	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs6076010	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6076012	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6076013	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6082974	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082975	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6082986	0.85[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6106596	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6113905	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6113908	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6515299	0.80[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7262749	0.80[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8120756	0.81[ASW][hapmap];0.80[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8125104	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs874585	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22991200-23002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr20:22994400-22999000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:22994600-22998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr20:22995600-22998600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:22995600-22999200	Enhancers	Dnd41	blood
6	chr20:22996000-23006200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:22996400-22998400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:22996600-22997600	Weak transcription	Fetal Thymus	thymus
9	chr20:22996600-22997600	Weak transcription	Thymus	Thymus
10	chr20:22996800-22998000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr20:22997200-22998600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr20:22997400-22997600	Enhancers	Brain Cingulate Gyrus	brain
13	chr20:22997400-22998000	Enhancers	Brain Substantia Nigra	brain
14	chr20:22997400-22998200	Enhancers	A549	lung

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