Variant report

Variant	rs346225
Chromosome Location	chr18:40028359-40028360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1036836	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1156542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12967873	1.00[YRI][hapmap]
rs1372762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1372763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1431834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs168300	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173196	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs180830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs180831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs180832	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs189389	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs189390	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2336238	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs237970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs237972	0.85[EUR][1000 genomes]
rs2584798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28760399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346182	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346185	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346186	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346187	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346188	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346189	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346190	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346191	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346193	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346194	0.83[EUR][1000 genomes]
rs346196	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346197	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346212	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346213	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346214	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs346215	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346217	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346218	0.88[EUR][1000 genomes]
rs346222	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346223	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346238	0.85[EUR][1000 genomes]
rs346261	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346263	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346264	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346265	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346266	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346268	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346269	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346270	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346271	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346438	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs346441	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs346442	0.85[EUR][1000 genomes]
rs346444	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs400064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs410555	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs417913	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs421138	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4312390	0.81[EUR][1000 genomes]
rs437300	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs437823	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441362	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445364	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4503884	0.82[EUR][1000 genomes]
rs4533372	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4575617	0.82[EUR][1000 genomes]
rs675137	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7226753	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7239965	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7241409	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72893563	0.83[EUR][1000 genomes]
rs72893564	0.83[EUR][1000 genomes]
rs72893572	0.80[EUR][1000 genomes]
rs72893580	0.81[EUR][1000 genomes]
rs72893582	0.81[EUR][1000 genomes]
rs72893596	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72903133	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72903135	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72907077	0.83[EUR][1000 genomes]
rs971293	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1059409	chr18:39711099-40139446	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv909572	chr18:39938510-40064000	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv3358540	chr18:40026748-40028962	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:40026200-40040000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr18:40026800-40028400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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