Variant report

Variant	rs1454124
Chromosome Location	chr7:124838438-124838439
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1020629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs10240611	0.97[ASN][1000 genomes]
rs10266152	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1031952	0.87[CHB][hapmap]
rs10500102	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap]
rs11761435	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs11771004	0.85[CHB][hapmap]
rs11771079	1.00[CHB][hapmap]
rs1248737	0.93[CHB][hapmap]
rs12531708	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534920	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12535063	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12539545	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357971	0.84[EUR][1000 genomes]
rs1404897	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs1471570	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1525620	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap]
rs1552116	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs1552117	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs17147889	0.87[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap]
rs17148021	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17148035	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28402853	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929322	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs34246481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs34974782	0.95[ASN][1000 genomes]
rs3847093	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58160159	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60486828	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612391	0.93[CHB][hapmap]
rs627823	0.93[CHB][hapmap]
rs6466995	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs650653	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs651988	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs663056	0.94[CHB][hapmap]
rs664062	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs6947036	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6954295	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6955284	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6965957	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6968595	0.95[ASN][1000 genomes]
rs715937	0.98[ASN][1000 genomes]
rs73438500	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73440504	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73440522	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73440528	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73440532	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73440534	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73440551	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7783242	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794583	0.83[EUR][1000 genomes]
rs7797011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7800299	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792617	0.98[ASN][1000 genomes]
rs792620	0.94[ASN][1000 genomes]
rs792637	0.98[ASN][1000 genomes]
rs967297	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs9785002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9942625	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]

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	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831119	chr7:124714009-124890119	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2422188	chr7:124782873-125254203	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1029627	chr7:124810399-124901651	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2761087	chr7:124823624-125429662	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1454124	CALU	cis	cerebellum	SCAN
rs1454124	POT1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124837600-124840000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:124838000-124838800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:124838400-124839400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:124838400-124839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:124838400-124839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:124838400-124839600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:124838400-124842000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:124838400-124842200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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