Variant report

Variant	rs28479828
Chromosome Location	chr4:79041455-79041456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10000651	0.85[ASN][1000 genomes]
rs10002604	0.91[ASN][1000 genomes]
rs10003965	0.94[ASN][1000 genomes]
rs10004159	0.94[ASN][1000 genomes]
rs10005735	0.94[ASN][1000 genomes]
rs10005862	0.86[ASN][1000 genomes]
rs10007371	0.88[ASN][1000 genomes]
rs10008931	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10010094	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10018454	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023589	0.83[AMR][1000 genomes]
rs10023665	0.83[AMR][1000 genomes]
rs10023697	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025194	0.94[ASN][1000 genomes]
rs10025611	0.94[ASN][1000 genomes]
rs10025769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025977	0.94[ASN][1000 genomes]
rs10026268	0.94[ASN][1000 genomes]
rs10028988	0.94[ASN][1000 genomes]
rs10029115	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029734	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10030639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031669	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10033428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213063	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213609	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518194	0.85[ASN][1000 genomes]
rs10856998	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11098038	0.90[EUR][1000 genomes]
rs13106100	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13106755	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13130161	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13133346	0.94[ASN][1000 genomes]
rs13136410	0.94[ASN][1000 genomes]
rs13144972	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150598	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317018	0.94[ASN][1000 genomes]
rs16997130	0.94[ASN][1000 genomes]
rs17002930	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17418552	0.88[ASN][1000 genomes]
rs17419053	0.88[ASN][1000 genomes]
rs1878437	0.94[ASN][1000 genomes]
rs1878438	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1878439	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2078481	0.94[ASN][1000 genomes]
rs28542863	0.81[ASN][1000 genomes]
rs28583476	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28597965	0.94[ASN][1000 genomes]
rs28635454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867004	0.88[ASN][1000 genomes]
rs2867006	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867008	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28671092	0.94[ASN][1000 genomes]
rs28677913	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707182	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750077	0.88[ASN][1000 genomes]
rs28750761	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28796316	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28822779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28854287	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2903452	0.94[ASN][1000 genomes]
rs2903453	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34552897	0.94[ASN][1000 genomes]
rs35374567	0.94[ASN][1000 genomes]
rs4156	0.92[EUR][1000 genomes]
rs4345212	0.94[EUR][1000 genomes]
rs4367202	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4388115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4410553	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4423899	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4423900	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4443313	0.89[EUR][1000 genomes]
rs4561952	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4583783	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4610363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55690666	0.94[ASN][1000 genomes]
rs55897032	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs56006343	0.83[EUR][1000 genomes]
rs56368720	0.94[ASN][1000 genomes]
rs58118093	0.88[ASN][1000 genomes]
rs58969863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58970756	0.88[ASN][1000 genomes]
rs66631138	0.94[ASN][1000 genomes]
rs6820400	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822247	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6838483	0.94[ASN][1000 genomes]
rs6838661	0.85[ASN][1000 genomes]
rs6840121	0.88[ASN][1000 genomes]
rs6840357	0.94[ASN][1000 genomes]
rs6842152	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6847174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6856815	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6857278	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857527	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858810	0.94[ASN][1000 genomes]
rs71609399	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654653	0.94[EUR][1000 genomes]
rs72654668	0.81[ASN][1000 genomes]
rs7437861	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7441634	0.98[EUR][1000 genomes]
rs7666444	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670625	0.94[ASN][1000 genomes]
rs7672583	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7673873	0.94[ASN][1000 genomes]
rs7677432	0.94[ASN][1000 genomes]
rs7681238	0.94[ASN][1000 genomes]
rs7684543	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689960	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7695979	0.94[ASN][1000 genomes]
rs7698326	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7699120	0.94[ASN][1000 genomes]
rs9307335	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307336	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307338	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307339	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307340	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307352	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9991356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993527	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994298	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995229	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998932	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9999763	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv520625	chr4:79002655-79071788	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79039600-79046800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:79039800-79046800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:79039800-79046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:79039800-79046800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:79039800-79047600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:79040800-79041800	Enhancers	Aorta	Aorta
7	chr4:79040800-79042000	Enhancers	Fetal Heart	heart
8	chr4:79040800-79043000	Enhancers	Psoas Muscle	Psoas
9	chr4:79040800-79043200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:79040800-79043200	Enhancers	HSMMtube	muscle
11	chr4:79041000-79042000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:79041000-79043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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