Variant report

Variant	rs12566690
Chromosome Location	chr1:57833868-57833869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10047071	0.86[ASN][1000 genomes]
rs10047073	0.86[ASN][1000 genomes]
rs10047177	0.81[ASN][1000 genomes]
rs10493219	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889042	0.82[ASN][1000 genomes]
rs10889044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11207020	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207021	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207022	0.91[ASN][1000 genomes]
rs11579258	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11581250	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585284	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585751	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11586826	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590652	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799925	0.83[ASN][1000 genomes]
rs12061812	0.85[ASN][1000 genomes]
rs12124445	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125219	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127603	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136107	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12137169	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12137540	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12137583	0.85[ASN][1000 genomes]
rs12139429	0.83[ASN][1000 genomes]
rs12142821	0.85[ASN][1000 genomes]
rs12405761	0.86[ASN][1000 genomes]
rs17115685	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17115686	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17424216	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17425017	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17456661	0.85[ASN][1000 genomes]
rs17457873	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17458730	0.82[ASN][1000 genomes]
rs17458751	0.82[ASN][1000 genomes]
rs17459384	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1778032	0.82[ASN][1000 genomes]
rs1778033	0.82[ASN][1000 genomes]
rs2052615	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2052616	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2052617	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113453	0.82[ASN][1000 genomes]
rs2113454	0.83[ASN][1000 genomes]
rs2216808	0.89[ASN][1000 genomes]
rs2405696	0.88[ASN][1000 genomes]
rs2405994	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3738553	0.86[ASN][1000 genomes]
rs3850549	0.82[ASN][1000 genomes]
rs3850550	0.82[ASN][1000 genomes]
rs3861834	0.82[ASN][1000 genomes]
rs3896279	0.82[ASN][1000 genomes]
rs3909556	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3909557	0.91[ASN][1000 genomes]
rs4912162	0.85[ASN][1000 genomes]
rs4912163	0.85[ASN][1000 genomes]
rs4912237	0.85[ASN][1000 genomes]
rs4912246	0.82[ASN][1000 genomes]
rs532926	0.82[ASN][1000 genomes]
rs539310	0.82[ASN][1000 genomes]
rs553674	0.82[ASN][1000 genomes]
rs55863020	0.85[ASN][1000 genomes]
rs564880	0.82[ASN][1000 genomes]
rs564951	0.82[ASN][1000 genomes]
rs565032	0.82[ASN][1000 genomes]
rs566847	0.82[ASN][1000 genomes]
rs61769670	0.83[ASN][1000 genomes]
rs61769725	0.89[ASN][1000 genomes]
rs6669975	0.88[ASN][1000 genomes]
rs6687842	0.83[ASN][1000 genomes]
rs6690017	0.87[ASN][1000 genomes]
rs72674872	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72674892	0.82[ASN][1000 genomes]
rs7513076	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528735	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535763	0.88[ASN][1000 genomes]
rs7540817	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57828600-57836800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57829600-57843400	Weak transcription	Fetal Heart	heart
3	chr1:57830200-57841800	Weak transcription	Fetal Brain Male	brain
4	chr1:57833000-57835800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57833200-57834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:57833200-57834400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:57833400-57834000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:57833600-57835000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57833800-57834600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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