Variant report

Variant	rs4660840
Chromosome Location	chr1:45668615-45668616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45660871..45664355-chr1:45665476..45670240,6	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1502340	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938299	1.00[AFR][1000 genomes]
rs2096435	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660298	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660299	0.85[EUR][1000 genomes]
rs4660837	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58612171	0.84[EUR][1000 genomes]
rs61788378	1.00[AFR][1000 genomes]
rs61788379	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61788380	1.00[AFR][1000 genomes]
rs61788382	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788383	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61788386	0.93[AMR][1000 genomes]
rs61788387	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788388	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788389	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61788390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788393	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788427	0.90[AMR][1000 genomes]
rs61788428	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61788429	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788430	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788436	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788438	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788439	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789773	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61789775	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61789785	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61789788	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789789	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61789808	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789809	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789814	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789816	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789817	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789818	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61789819	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789820	0.85[EUR][1000 genomes]
rs61789821	0.85[EUR][1000 genomes]
rs61789822	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61789826	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61789830	1.00[AFR][1000 genomes]
rs6429564	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45660000-45670800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45666800-45669400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:45667200-45669400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:45668000-45673800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:45668400-45668800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:45668400-45669400	Active TSS	Brain Germinal Matrix	brain
7	chr1:45668400-45670000	Enhancers	Fetal Brain Male	brain
8	chr1:45668400-45670000	Enhancers	Hela-S3	cervix
9	chr1:45668600-45669400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:45668600-45669800	Flanking Active TSS	HepG2	liver
11	chr1:45668600-45672800	Active TSS	Fetal Brain Female	brain

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