Variant report

Variant	rs28871899
Chromosome Location	chr4:79317957-79317958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10000275	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10008117	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010238	0.94[ASN][1000 genomes]
rs10015470	0.94[ASN][1000 genomes]
rs10015547	0.94[ASN][1000 genomes]
rs10016220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032457	0.94[ASN][1000 genomes]
rs10155231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098146	0.94[ASN][1000 genomes]
rs11098162	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11721347	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642918	0.84[ASN][1000 genomes]
rs12643134	0.94[ASN][1000 genomes]
rs12643552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113556	0.92[EUR][1000 genomes]
rs13114164	0.94[ASN][1000 genomes]
rs13114483	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123934	0.97[ASN][1000 genomes]
rs13124000	0.97[ASN][1000 genomes]
rs13131912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454890	0.94[ASN][1000 genomes]
rs1454891	0.94[ASN][1000 genomes]
rs1484339	0.97[ASN][1000 genomes]
rs1484346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484348	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003131	0.88[ASN][1000 genomes]
rs17003164	0.94[ASN][1000 genomes]
rs1973256	0.97[ASN][1000 genomes]
rs2004557	0.82[ASN][1000 genomes]
rs2008453	0.94[ASN][1000 genomes]
rs28623348	0.94[ASN][1000 genomes]
rs28645909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654799	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28685810	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28756791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826318	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28868898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28891759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34141392	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34193629	0.91[ASN][1000 genomes]
rs34204048	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345543	0.94[ASN][1000 genomes]
rs34568699	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35050841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35514354	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35610069	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365543	0.97[ASN][1000 genomes]
rs365657	0.94[ASN][1000 genomes]
rs366463	0.97[ASN][1000 genomes]
rs367885	0.91[ASN][1000 genomes]
rs368313	0.94[ASN][1000 genomes]
rs370865	0.91[ASN][1000 genomes]
rs371716	0.94[ASN][1000 genomes]
rs372736	0.94[ASN][1000 genomes]
rs374822	0.97[ASN][1000 genomes]
rs376200	0.94[ASN][1000 genomes]
rs380076	0.94[ASN][1000 genomes]
rs381503	0.97[ASN][1000 genomes]
rs385285	0.97[ASN][1000 genomes]
rs385809	0.94[ASN][1000 genomes]
rs386832	0.91[ASN][1000 genomes]
rs387122	0.94[ASN][1000 genomes]
rs388825	0.91[ASN][1000 genomes]
rs395186	0.94[ASN][1000 genomes]
rs402843	0.94[ASN][1000 genomes]
rs408224	0.94[ASN][1000 genomes]
rs408835	0.94[ASN][1000 genomes]
rs409061	0.94[ASN][1000 genomes]
rs410769	0.94[ASN][1000 genomes]
rs412797	0.94[ASN][1000 genomes]
rs415472	0.94[ASN][1000 genomes]
rs417621	0.97[ASN][1000 genomes]
rs423638	0.94[ASN][1000 genomes]
rs425699	0.97[ASN][1000 genomes]
rs427539	0.97[ASN][1000 genomes]
rs429977	0.97[ASN][1000 genomes]
rs431664	0.97[ASN][1000 genomes]
rs435317	0.97[ASN][1000 genomes]
rs437057	0.94[ASN][1000 genomes]
rs4386625	0.88[ASN][1000 genomes]
rs444500	0.91[ASN][1000 genomes]
rs445071	0.94[ASN][1000 genomes]
rs445869	0.91[ASN][1000 genomes]
rs445963	0.91[ASN][1000 genomes]
rs448353	0.97[ASN][1000 genomes]
rs452319	0.91[ASN][1000 genomes]
rs454498	0.97[ASN][1000 genomes]
rs454551	0.97[ASN][1000 genomes]
rs569894	0.94[ASN][1000 genomes]
rs58220389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672608	0.94[ASN][1000 genomes]
rs71611019	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72866338	0.88[ASN][1000 genomes]
rs72866340	0.88[ASN][1000 genomes]
rs72866341	0.88[ASN][1000 genomes]
rs72866344	0.88[ASN][1000 genomes]
rs72866346	0.82[ASN][1000 genomes]
rs72866347	0.88[ASN][1000 genomes]
rs72866348	0.88[ASN][1000 genomes]
rs72866349	0.91[ASN][1000 genomes]
rs7656232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693638	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
2	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
3	chr4:79291800-79318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:79302400-79353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:79308800-79318600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:79309000-79331000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:79309200-79318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:79309200-79334800	Weak transcription	Fetal Heart	heart
10	chr4:79310000-79330800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:79310800-79321800	Weak transcription	HepG2	liver
12	chr4:79311000-79318400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:79311000-79318400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:79311000-79334600	Weak transcription	Fetal Lung	lung
15	chr4:79312000-79318200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:79314000-79318400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:79316600-79318000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr4:79317200-79318000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:79317200-79318000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:79317600-79318200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:79317600-79318200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr4:79317600-79319000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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