Variant report

Variant	rs3795251
Chromosome Location	chr1:76397972-76397973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76260266..76263027-chr1:76396916..76399571,2	K562	blood:

Variant related genes	Relation type
ENSG00000057468	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1021462	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10465725	0.93[YRI][hapmap]
rs10732724	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10873738	0.85[JPT][hapmap]
rs10873804	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161602	0.91[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap]
rs11161731	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11161852	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11161872	0.93[YRI][hapmap]
rs11161887	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1146635	0.83[GIH][hapmap]
rs1146648	0.81[JPT][hapmap]
rs1146651	0.80[JPT][hapmap]
rs12021750	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12022011	0.81[CHB][hapmap]
rs12022506	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12024645	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs12032051	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs12033058	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12043473	0.81[GIH][hapmap]
rs12044025	0.86[JPT][hapmap]
rs12044211	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12076093	0.81[JPT][hapmap]
rs12086506	0.89[YRI][hapmap]
rs12089337	0.87[YRI][hapmap]
rs12090389	0.93[YRI][hapmap]
rs12090712	0.80[JPT][hapmap]
rs12164500	0.87[CEU][hapmap];0.91[YRI][hapmap]
rs12401729	0.81[JPT][hapmap]
rs12402230	0.81[ASN][1000 genomes]
rs12407107	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs12409592	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs12410373	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251581	0.83[ASN][1000 genomes]
rs1251587	0.83[ASN][1000 genomes]
rs1251594	0.81[ASN][1000 genomes]
rs12567390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12732495	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12744608	0.81[CHB][hapmap]
rs1303870	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1498313	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1572859	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1603734	0.81[JPT][hapmap]
rs1689271	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17097681	0.86[JPT][hapmap]
rs17097695	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17097696	0.93[YRI][hapmap]
rs17097710	0.83[LWK][hapmap];0.93[YRI][hapmap]
rs17649675	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796812	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1873894	0.80[ASN][1000 genomes]
rs1908089	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2028212	0.95[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307077	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs35290302	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs3737574	0.91[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs3765682	0.81[JPT][hapmap]
rs3819949	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]
rs5745309	0.81[YRI][hapmap]
rs5745314	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5745334	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5745429	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs5745448	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs5745451	0.85[JPT][hapmap]
rs5745464	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs5745465	0.81[JPT][hapmap]
rs5745496	0.93[YRI][hapmap]
rs5745516	0.83[LWK][hapmap];0.93[YRI][hapmap]
rs5745523	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs5745532	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs5745542	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs5745546	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6593520	0.83[GIH][hapmap]
rs6685657	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687882	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6693002	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514912	0.81[JPT][hapmap]
rs7520312	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524665	0.81[ASN][1000 genomes]
rs7525919	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7545057	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7548391	0.81[JPT][hapmap]
rs7548991	0.86[CHB][hapmap]
rs931506	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9660848	0.86[CHB][hapmap]
rs9970840	0.80[LWK][hapmap];0.81[YRI][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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3795251	SNORD45B	cis	cerebellum	SCAN
rs3795251	MSH4	cis	parietal	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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