Variant report

Variant	rs2553460
Chromosome Location	chr4:106732183-106732184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10017111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10023798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10516520	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs10516521	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10516524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11097896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1294668	0.94[ASN][1000 genomes]
rs1294671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1294672	0.94[ASN][1000 genomes]
rs1447093	0.83[CEU][hapmap]
rs1447094	0.85[CEU][hapmap]
rs17260120	1.00[JPT][hapmap]
rs17260183	1.00[JPT][hapmap]
rs17260856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17261786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17262443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17262457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17263714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17264527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1862081	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1982346	0.83[ASN][1000 genomes]
rs2098571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2112047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2112052	0.87[YRI][hapmap]
rs2161046	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2193855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2193856	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193857	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2216515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216516	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256746	1.00[ASN][1000 genomes]
rs2305212	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544399	1.00[ASN][1000 genomes]
rs2544401	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs2544402	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2544414	0.94[ASN][1000 genomes]
rs2544417	0.93[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544418	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2544424	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2544426	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2544429	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2544430	1.00[ASN][1000 genomes]
rs2553446	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2553452	0.94[ASN][1000 genomes]
rs2553456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2553461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2553466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2553467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2553469	1.00[ASN][1000 genomes]
rs2553470	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2553471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2866781	0.86[ASW][hapmap];1.00[ASN][1000 genomes]
rs3796920	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796923	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3943980	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56843185	0.94[ASN][1000 genomes]
rs6833345	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73837092	0.83[ASN][1000 genomes]
rs73837096	0.83[ASN][1000 genomes]
rs73839004	0.94[ASN][1000 genomes]
rs73839006	0.94[ASN][1000 genomes]
rs73839007	0.94[ASN][1000 genomes]
rs73839008	0.94[ASN][1000 genomes]
rs73839010	0.94[ASN][1000 genomes]
rs7676226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7698817	1.00[JPT][hapmap]
rs961472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs961473	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879700	chr4:106643445-106745057	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106695200-106757000	Weak transcription	Primary B cells from cord blood	blood
2	chr4:106703200-106755600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:106724200-106736400	Weak transcription	Ovary	ovary
4	chr4:106729200-106763400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:106730200-106764200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:106730400-106732200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:106730400-106732400	Weak transcription	HMEC	breast
8	chr4:106730400-106738800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:106730400-106756400	Weak transcription	Fetal Stomach	stomach
10	chr4:106730400-106757600	Weak transcription	Psoas Muscle	Psoas
11	chr4:106730800-106736200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:106730800-106761800	Weak transcription	HSMM	muscle
13	chr4:106732000-106732200	Enhancers	Cortex derived primary cultured neurospheres	brain

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