Variant report

Variant	rs1497907
Chromosome Location	chr4:62433777-62433778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10018746	0.82[CHB][hapmap]
rs10031433	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10866123	0.84[ASN][1000 genomes]
rs10866124	0.86[ASW][hapmap];0.87[CHD][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11131329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11131330	0.85[CHB][hapmap]
rs11131334	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11735278	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11939481	0.92[CEU][hapmap]
rs11941524	0.84[ASN][1000 genomes]
rs12504607	0.92[CEU][hapmap]
rs12715703	0.93[ASN][1000 genomes]
rs12715704	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123468	0.92[CEU][hapmap]
rs13123888	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1391321	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1472425	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1497901	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1497906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1497909	0.89[CEU][hapmap]
rs1497916	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1497921	0.92[CEU][hapmap]
rs1603660	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17239080	0.86[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1846160	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2172802	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2343250	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4860417	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860418	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60279254	0.82[ASN][1000 genomes]
rs6551634	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6551637	0.92[CEU][hapmap]
rs6551640	0.92[CEU][hapmap]
rs67669396	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6813075	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6817476	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6835374	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6843311	0.89[CEU][hapmap]
rs6851424	0.92[CEU][hapmap]
rs72614740	0.83[ASN][1000 genomes]
rs72614741	0.82[ASN][1000 genomes]
rs7656051	0.92[CEU][hapmap]
rs7669283	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs958862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9685140	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9991244	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2753138	chr4:62271444-62442507	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1004815	chr4:62398737-62553769	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv537110	chr4:62398737-62553769	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1004432	chr4:62408333-62444506	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv537111	chr4:62408333-62444506	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv594329	chr4:62416593-62478230	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv879077	chr4:62419426-62545435	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1497907	LPHN3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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