Variant report

Variant	rs1858536
Chromosome Location	chr1:76161595-76161596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76158932..76160525-chr1:76160690..76162510,2	K562	blood:
2	chr1:76160863..76164413-chr1:76188361..76190736,3	K562	blood:

Variant related genes	Relation type
ENSG00000117054	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1061337	0.85[EUR][1000 genomes]
rs10873685	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11161437	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161468	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11161493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161510	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11161511	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11161515	0.86[EUR][1000 genomes]
rs11161521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11161620	0.81[TSI][hapmap]
rs11163924	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1146579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1146580	0.94[EUR][1000 genomes]
rs1146581	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs1146588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1146646	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs12091720	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12094842	0.82[EUR][1000 genomes]
rs12122939	0.81[TSI][hapmap]
rs12123977	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12126481	0.82[EUR][1000 genomes]
rs12126607	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12127402	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12134854	0.96[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];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1250874	0.94[EUR][1000 genomes]
rs1251075	0.94[EUR][1000 genomes]
rs1251077	0.80[AFR][1000 genomes]
rs1251078	0.96[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs1251079	0.86[ASW][hapmap];0.96[CEU][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs1303169	0.92[EUR][1000 genomes]
rs1313071	0.93[EUR][1000 genomes]
rs1498312	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1611823	0.94[EUR][1000 genomes]
rs1612097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1613437	0.84[EUR][1000 genomes]
rs1694419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1694424	0.89[EUR][1000 genomes]
rs17587071	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1767455	0.89[EUR][1000 genomes]
rs1767456	0.94[EUR][1000 genomes]
rs1767458	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1770511	0.93[EUR][1000 genomes]
rs1855136	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890451	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1890452	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2066183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211717	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211718	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211737	1.00[ASN][1000 genomes]
rs2153126	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2173378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2185152	0.86[EUR][1000 genomes]
rs2185435	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2185436	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2275378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2788654	0.94[EUR][1000 genomes]
rs28602663	0.82[EUR][1000 genomes]
rs380075	0.95[ASN][1000 genomes]
rs3818855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392691	1.00[ASN][1000 genomes]
rs4559448	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4646961	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949674	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949872	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.96[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];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949877	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949879	0.81[EUR][1000 genomes]
rs57186386	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60378926	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289992	0.85[EUR][1000 genomes]
rs61622554	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61797339	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61797340	0.86[EUR][1000 genomes]
rs61799967	0.86[EUR][1000 genomes]
rs61799969	0.82[EUR][1000 genomes]
rs6593514	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6593515	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6593585	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688749	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72686191	0.85[EUR][1000 genomes]
rs7513363	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515955	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7516122	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516226	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs7518038	0.96[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];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524467	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7535991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539246	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7541058	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7544117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547056	0.81[TSI][hapmap]
rs7548962	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549167	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550974	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7552404	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554984	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8763	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs942270	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9662166	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv945914	chr1:76109781-76172388	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1858536	SNORD45B	cis	cerebellum	SCAN
rs1858536	CRYZ	cis	cerebellum	SCAN
rs1858536	MSH4	cis	Artery Tibial	GTEx
rs1858536	MSH4	cis	parietal	SCAN
rs1858536	SNORD45B	cis	parietal	SCAN
rs1858536	ACADM	cis	cerebellum	SCAN
rs1858536	DISP2	trans	cerebellum	SCAN

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

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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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