Variant report

Variant	rs1821119
Chromosome Location	chr20:23052282-23052283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23050588..23053168-chr20:23056327..23058098,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD93-5	chr20:23052184-23053359	NONHSAT079032
2	lnc-SSTR4-9	chr20:23052184-23053787	NONHSAT079031

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040588	0.90[EUR][1000 genomes]
rs1835702	0.89[EUR][1000 genomes]
rs1835703	0.86[EUR][1000 genomes]
rs1835704	0.88[EUR][1000 genomes]
rs1998079	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1998080	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2007743	0.88[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2019632	0.91[EUR][1000 genomes]
rs2144939	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2207110	0.80[EUR][1000 genomes]
rs2255937	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2424503	0.89[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2424509	0.92[EUR][1000 genomes]
rs2424510	0.92[EUR][1000 genomes]
rs2424511	0.84[EUR][1000 genomes]
rs2567619	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2749813	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2749817	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036291	0.92[EUR][1000 genomes]
rs6048519	0.85[CEU][hapmap]
rs6048526	0.92[EUR][1000 genomes]
rs6048533	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6076016	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[EUR][1000 genomes]
rs6082997	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083000	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3346177	chr20:23048710-23052980	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1821119	THBD	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23043400-23063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23043600-23053000	Weak transcription	Ovary	ovary
3	chr20:23043600-23054000	Weak transcription	Lung	lung
4	chr20:23043600-23062200	Weak transcription	Placenta	Placenta
5	chr20:23043600-23066600	Weak transcription	Aorta	Aorta
6	chr20:23043800-23055200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr20:23044800-23053000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr20:23046600-23052600	Weak transcription	Fetal Lung	lung
9	chr20:23047200-23057800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr20:23047800-23059000	Weak transcription	Right Atrium	heart
11	chr20:23050800-23061200	Weak transcription	Esophagus	oesophagus
12	chr20:23051200-23055000	Weak transcription	Primary T cells from cord blood	blood
13	chr20:23051800-23058400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links