Variant report

Variant	rs1400660
Chromosome Location	chr2:116133379-116133380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10165687	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10167944	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180987	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10181472	0.82[ASN][1000 genomes]
rs10181696	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10451600	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496490	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496491	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123302	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1155664	0.81[ASN][1000 genomes]
rs1159302	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678564	0.85[ASN][1000 genomes]
rs11883530	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11896853	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11898241	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11898436	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11902350	0.81[ASN][1000 genomes]
rs12474916	0.82[ASN][1000 genomes]
rs12478263	0.84[ASN][1000 genomes]
rs12478502	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12611770	0.84[ASN][1000 genomes]
rs13017848	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400662	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400663	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400667	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1400668	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1402445	0.85[ASN][1000 genomes]
rs1517361	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1517362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517371	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1521071	0.81[ASN][1000 genomes]
rs1521075	0.84[ASN][1000 genomes]
rs1607914	0.85[ASN][1000 genomes]
rs1949402	0.84[ASN][1000 genomes]
rs2176955	0.81[ASN][1000 genomes]
rs2420819	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421100	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268936	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4610067	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4614945	0.81[ASN][1000 genomes]
rs4849396	0.81[ASN][1000 genomes]
rs62167292	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62167293	0.84[ASN][1000 genomes]
rs6542259	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714356	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6716722	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6726183	0.81[ASN][1000 genomes]
rs6749876	0.81[ASN][1000 genomes]
rs6760151	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7422121	0.83[ASN][1000 genomes]
rs7561031	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7564387	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7571103	0.83[ASN][1000 genomes]
rs7578669	0.81[ASN][1000 genomes]
rs7589983	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908600	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs949889	0.81[ASN][1000 genomes]
rs963850	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963851	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs992217	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs992218	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs993986	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[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	nsv874918	chr2:116098665-116183946	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
2	nsv963924	chr2:116110836-116134022	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv874919	chr2:116130709-116219686	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	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	chr2:116130000-116134000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:116130200-116133600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr2:116130200-116133600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:116130200-116134000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr2:116130800-116133800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr2:116131600-116133800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
7	chr2:116131800-116133800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:116131800-116133800	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr2:116131800-116134000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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