Variant report

Variant	rs269054
Chromosome Location	chr1:57864304-57864305
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10493221	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889042	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10889043	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889044	0.87[ASN][1000 genomes]
rs11207022	0.81[EUR][1000 genomes]
rs11207024	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207025	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207026	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207027	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11207028	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207029	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11585751	0.87[ASN][1000 genomes]
rs11803514	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12092706	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137169	0.87[ASN][1000 genomes]
rs17115750	0.93[ASN][1000 genomes]
rs17458730	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17458751	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17459384	0.87[ASN][1000 genomes]
rs1778032	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1778033	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2405994	0.87[ASN][1000 genomes]
rs269044	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs269045	0.89[ASN][1000 genomes]
rs269048	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs269049	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs269050	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs269051	0.82[ASN][1000 genomes]
rs269057	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738553	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3844041	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850549	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850550	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850552	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850556	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3861834	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3896279	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3909557	0.81[EUR][1000 genomes]
rs4912246	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912247	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs511115	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs515148	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs516918	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517825	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532926	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs539310	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs540431	0.89[ASN][1000 genomes]
rs553674	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs563099	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs563270	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564880	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564951	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565032	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566847	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61769756	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587768	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72674892	0.85[EUR][1000 genomes];0.83[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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57858000-57868600	Weak transcription	Fetal Brain Male	brain
2	chr1:57860200-57865400	Weak transcription	HepG2	liver
3	chr1:57860200-57865600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:57860400-57874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:57862400-57870800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:57862400-57873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57863400-57864400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:57863800-57875400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:57864000-57864400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:57864000-57867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:57864000-57867400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:57864200-57867200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:57864200-57867200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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