Variant report

Variant	rs10016220
Chromosome Location	chr4:79308446-79308447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10000275	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10008117	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[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]
rs10018431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032457	0.94[ASN][1000 genomes]
rs10155231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098146	0.94[ASN][1000 genomes]
rs11098162	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11721347	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642918	0.84[ASN][1000 genomes]
rs12643134	0.94[ASN][1000 genomes]
rs12643552	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113556	0.91[EUR][1000 genomes]
rs13114164	0.94[ASN][1000 genomes]
rs13114483	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123934	0.97[ASN][1000 genomes]
rs13124000	0.97[ASN][1000 genomes]
rs13131912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654799	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28685810	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28756791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28868898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28871899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28891759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34141392	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34193629	0.91[ASN][1000 genomes]
rs34204048	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345543	0.94[ASN][1000 genomes]
rs34568699	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35050841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35514354	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35610069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672608	0.94[ASN][1000 genomes]
rs71611019	0.95[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693638	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923017	0.92[YRI][hapmap]
rs923019	0.89[YRI][hapmap]
rs9307386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79275400-79310600	Weak transcription	Aorta	Aorta
2	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
3	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
4	chr4:79290200-79310800	Weak transcription	Brain Anterior Caudate	brain
5	chr4:79291200-79314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:79291800-79318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:79292000-79312000	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr4:79292200-79312200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:79292400-79310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:79292400-79312000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:79297600-79310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:79299400-79308600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:79300800-79313200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:79302000-79311000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:79302400-79308600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:79302400-79308600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:79302400-79310800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:79302400-79312200	Weak transcription	HSMMtube	muscle
20	chr4:79302400-79315400	Weak transcription	Psoas Muscle	Psoas
21	chr4:79302400-79315600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:79302400-79353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:79305600-79308600	Weak transcription	Lung	lung
24	chr4:79306200-79308600	Weak transcription	Fetal Intestine Small	intestine
25	chr4:79307400-79309800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:79307600-79311200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:79308000-79308600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:79308000-79308800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:79308000-79311000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr4:79308000-79311200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:79308200-79310800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:79308200-79310800	Strong transcription	Fetal Kidney	kidney
33	chr4:79308400-79309000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:79308400-79309000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:79308400-79309200	Strong transcription	Fetal Heart	heart
36	chr4:79308400-79309400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:79308400-79310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:79308400-79310800	Strong transcription	HepG2	liver
39	chr4:79308400-79311000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:79308400-79311000	Strong transcription	Fetal Intestine Large	intestine
41	chr4:79308400-79311000	Strong transcription	Fetal Lung	lung
42	chr4:79308400-79312000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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