Variant report

Variant	rs4599408
Chromosome Location	chr4:21088345-21088346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10014546	0.85[ASN][1000 genomes]
rs10022535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032561	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10433822	0.85[ASN][1000 genomes]
rs10805223	0.83[JPT][hapmap]
rs10938824	0.84[JPT][hapmap]
rs10938827	0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10938831	0.85[ASN][1000 genomes]
rs11735843	0.85[ASN][1000 genomes]
rs11735844	0.85[ASN][1000 genomes]
rs11736507	0.85[ASN][1000 genomes]
rs11736572	0.85[ASN][1000 genomes]
rs11935122	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11944165	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11945600	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11945646	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11945692	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12510687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12639638	0.85[ASN][1000 genomes]
rs12640310	0.85[ASN][1000 genomes]
rs12640491	0.87[CHB][hapmap]
rs12642886	0.85[ASN][1000 genomes]
rs12644882	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12644941	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12645002	0.83[JPT][hapmap]
rs12646316	0.85[ASN][1000 genomes]
rs12647437	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1368646	0.85[ASN][1000 genomes]
rs1368648	0.85[ASN][1000 genomes]
rs17574283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17636197	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap]
rs17637027	0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2043387	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2043388	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2163931	0.83[ASN][1000 genomes]
rs2163933	0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs2163934	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs28406534	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4572877	0.85[ASN][1000 genomes]
rs4574407	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs4590029	0.85[ASN][1000 genomes]
rs4615170	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55737345	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55885656	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55957496	0.83[ASN][1000 genomes]
rs56025335	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56139613	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56412118	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58548088	0.85[ASN][1000 genomes]
rs59223154	0.85[ASN][1000 genomes]
rs59416831	0.85[ASN][1000 genomes]
rs60444813	0.85[ASN][1000 genomes]
rs61644618	0.85[ASN][1000 genomes]
rs6810466	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810897	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817687	0.80[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818751	0.84[JPT][hapmap]
rs6819439	0.84[JPT][hapmap]
rs6832569	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832607	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845231	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6853609	0.84[JPT][hapmap]
rs6854888	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6855710	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6858766	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs720852	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs720853	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs73802481	0.85[ASN][1000 genomes]
rs7658908	0.85[ASN][1000 genomes]
rs9997060	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv829878	chr4:20966047-21138626	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv878745	chr4:21054348-21155716	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv878746	chr4:21054348-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv878747	chr4:21057794-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv522328	chr4:21083553-21096827	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21085800-21089800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:21086000-21089600	Weak transcription	HUVEC	blood vessel

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