Variant report

Variant	rs38725
Chromosome Location	chr7:140699420-140699421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS33-2	chr7:140698982-140699600	NONHSAT123700

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10271387	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279193	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1089265	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1091374	1.00[ASN][1000 genomes]
rs1091557	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12534351	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534354	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860481	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079829	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246738	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246740	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246742	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246743	0.92[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246744	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246745	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs246746	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2533300	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2533307	1.00[ASN][1000 genomes]
rs2533308	1.00[ASN][1000 genomes]
rs2688429	1.00[ASN][1000 genomes]
rs3844322	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38716	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38721	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38724	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs38727	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38728	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38729	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38733	1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs38737	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38741	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38743	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4020017	1.00[ASN][1000 genomes]
rs4020018	1.00[ASN][1000 genomes]
rs4726134	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486595	0.80[AFR][1000 genomes]
rs62486599	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6949856	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950813	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71645926	1.00[ASN][1000 genomes]
rs7778860	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787917	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs801096	1.00[ASN][1000 genomes]
rs801097	1.00[ASN][1000 genomes]
rs801118	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs801119	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs801122	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs801124	0.98[EUR][1000 genomes]
rs801126	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9640306	0.85[EUR][1000 genomes];1.00[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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38725	TMEM178B	cis	Esophagus Mucosa	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140697800-140701600	Enhancers	HepG2	liver
2	chr7:140698400-140705400	Weak transcription	Fetal Lung	lung
3	chr7:140698600-140713000	Weak transcription	Psoas Muscle	Psoas
4	chr7:140699000-140704000	Enhancers	Fetal Intestine Large	intestine
5	chr7:140699400-140699600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:140699400-140703800	Enhancers	Fetal Intestine Small	intestine

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