Variant report

Variant	rs2553458
Chromosome Location	chr4:106737796-106737797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10025790	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs10516523	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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11722731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11933386	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11933466	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11934139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941690	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12639750	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1294670	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1294673	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120110	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13148869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17036098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17262764	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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044536	0.82[CEU][hapmap];0.95[CHD][hapmap]
rs2080789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544395	0.86[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];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2544404	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2544405	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2544406	0.82[CHB][hapmap]
rs2544408	0.82[CHB][hapmap]
rs2544409	0.82[CHB][hapmap]
rs2544412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544413	1.00[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544421	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2544423	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2544425	0.82[CHB][hapmap]
rs2553432	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2553436	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2553438	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2553441	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553445	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2553449	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2553453	0.82[CHB][hapmap]
rs2553462	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628106	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756260	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4699196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533218	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533221	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6820200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7684839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7685231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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:14 , 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	chr4:106729200-106763400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:106730200-106764200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:106730400-106738800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:106730400-106756400	Weak transcription	Fetal Stomach	stomach
7	chr4:106730400-106757600	Weak transcription	Psoas Muscle	Psoas
8	chr4:106730800-106761800	Weak transcription	HSMM	muscle
9	chr4:106732600-106755800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:106734400-106756400	Weak transcription	Fetal Thymus	thymus
11	chr4:106734800-106746600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:106735800-106747800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:106737000-106768600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:106737200-106754200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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