Variant report

Variant	rs6690017
Chromosome Location	chr1:57842729-57842730
allele	G/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:75)

rs_ID	r²[population]
rs10047071	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10047072	0.88[ASN][1000 genomes]
rs10047073	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10047177	0.90[ASN][1000 genomes]
rs10047179	0.87[ASN][1000 genomes]
rs10493219	0.89[ASN][1000 genomes]
rs10889039	0.83[ASN][1000 genomes]
rs10889041	0.88[ASN][1000 genomes]
rs11207010	0.83[ASN][1000 genomes]
rs11207016	0.81[ASN][1000 genomes]
rs11207018	0.83[ASN][1000 genomes]
rs11207020	0.87[ASN][1000 genomes]
rs11207021	0.89[ASN][1000 genomes]
rs11207022	0.82[ASN][1000 genomes]
rs11579258	0.89[ASN][1000 genomes]
rs11581250	0.89[ASN][1000 genomes]
rs11585284	0.89[ASN][1000 genomes]
rs11586826	0.89[ASN][1000 genomes]
rs11590652	0.86[ASN][1000 genomes]
rs11590708	0.81[ASN][1000 genomes]
rs12067263	0.88[ASN][1000 genomes]
rs12087888	0.83[ASN][1000 genomes]
rs12119210	0.81[ASN][1000 genomes]
rs12124445	0.89[ASN][1000 genomes]
rs12125219	0.89[ASN][1000 genomes]
rs12126723	0.81[ASN][1000 genomes]
rs12127603	0.89[ASN][1000 genomes]
rs12136107	0.89[ASN][1000 genomes]
rs12137540	0.84[ASN][1000 genomes]
rs12240237	0.81[ASN][1000 genomes]
rs1240442	0.88[ASN][1000 genomes]
rs1240443	0.88[ASN][1000 genomes]
rs12405761	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565446	0.81[ASN][1000 genomes]
rs12565636	0.81[ASN][1000 genomes]
rs12566690	0.87[ASN][1000 genomes]
rs1364444	0.81[ASN][1000 genomes]
rs1424462	0.81[ASN][1000 genomes]
rs1424463	0.81[ASN][1000 genomes]
rs1424464	0.81[ASN][1000 genomes]
rs1424467	0.81[ASN][1000 genomes]
rs1424468	0.81[ASN][1000 genomes]
rs1424469	0.81[ASN][1000 genomes]
rs1424470	0.81[ASN][1000 genomes]
rs1557222	0.88[ASN][1000 genomes]
rs17115685	0.89[ASN][1000 genomes]
rs17115686	0.89[ASN][1000 genomes]
rs17423255	0.81[ASN][1000 genomes]
rs17424216	0.89[ASN][1000 genomes]
rs17425017	0.81[ASN][1000 genomes]
rs17457873	0.89[ASN][1000 genomes]
rs1834151	0.81[ASN][1000 genomes]
rs2052615	0.86[ASN][1000 genomes]
rs2052616	0.86[ASN][1000 genomes]
rs2052617	0.89[ASN][1000 genomes]
rs2113453	0.87[ASN][1000 genomes]
rs2216808	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405697	0.88[ASN][1000 genomes]
rs267650	0.83[ASN][1000 genomes]
rs269038	0.88[ASN][1000 genomes]
rs269039	0.88[ASN][1000 genomes]
rs3861833	0.88[ASN][1000 genomes]
rs3909556	0.89[ASN][1000 genomes]
rs3909557	0.82[ASN][1000 genomes]
rs3909558	0.88[ASN][1000 genomes]
rs567773	0.81[ASN][1000 genomes]
rs61769725	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665166	0.80[ASN][1000 genomes]
rs6669975	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677561	0.81[ASN][1000 genomes]
rs7513076	0.84[ASN][1000 genomes]
rs7528735	0.87[ASN][1000 genomes]
rs7535763	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540817	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57829600-57843400	Weak transcription	Fetal Heart	heart
2	chr1:57834800-57843200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:57835000-57843200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:57835800-57843000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57837000-57843200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:57837400-57847600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:57837600-57843200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:57841600-57843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:57841800-57844000	Enhancers	Fetal Brain Male	brain

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