Variant report

Variant	rs6855645
Chromosome Location	chr4:173557163-173557164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGB2-13	chr4:173555835-173557753	NONHSAT099210

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10016145	0.91[CHB][hapmap]
rs1017667	0.82[CEU][hapmap]
rs10434280	0.84[CEU][hapmap]
rs10866355	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10866356	0.84[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs1106651	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11132951	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs11132952	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap]
rs11132954	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs11132955	0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs11132959	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs11132964	0.82[MEX][hapmap]
rs11132967	0.82[MEX][hapmap]
rs1158684	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722378	0.83[ASN][1000 genomes]
rs11725400	0.84[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs11942645	0.82[MEX][hapmap]
rs12499508	0.82[CEU][hapmap]
rs12501331	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12503858	0.81[CEU][hapmap]
rs12509744	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12642131	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap]
rs12642442	0.84[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs12645987	0.82[GIH][hapmap]
rs12647340	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs12649403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12649426	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs13102637	0.81[CEU][hapmap]
rs13107045	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13123441	0.81[CEU][hapmap]
rs13134194	0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs13146563	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1347700	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1347702	0.82[CHD][hapmap]
rs1370581	0.83[ASN][1000 genomes]
rs1437834	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1437837	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1437842	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1455132	0.82[CEU][hapmap]
rs1540466	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs1540470	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1548346	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs1580110	0.82[CEU][hapmap]
rs17058876	0.82[MEX][hapmap]
rs17234582	0.81[CEU][hapmap]
rs17307651	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs17308839	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17308944	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1898554	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2118439	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2118442	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2332544	0.82[GIH][hapmap]
rs34567973	0.83[ASN][1000 genomes]
rs35280724	0.83[ASN][1000 genomes]
rs35345168	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35640087	0.85[CEU][hapmap]
rs4470604	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4476577	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs4546224	0.84[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4569731	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs4608790	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4692921	0.81[CEU][hapmap]
rs4695771	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4695799	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4695878	0.88[CEU][hapmap]
rs4696006	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4696015	0.83[ASN][1000 genomes]
rs4696016	0.83[ASN][1000 genomes]
rs4696028	0.82[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs55850929	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6553645	0.82[ASN][1000 genomes]
rs6817631	0.82[MEX][hapmap]
rs6819441	0.83[ASN][1000 genomes]
rs6822571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6839760	0.82[CEU][hapmap]
rs6858309	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs7438724	0.90[CHB][hapmap]
rs748347	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7658615	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs7659511	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7672525	0.81[CEU][hapmap]
rs7672787	0.83[ASN][1000 genomes]
rs7681189	0.82[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs7691448	0.83[ASN][1000 genomes]
rs7696315	0.81[CEU][hapmap]
rs837196	0.81[CHD][hapmap]
rs9312534	0.82[MEX][hapmap]
rs9997085	0.83[MEX][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	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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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