Variant report

Variant	rs55684284
Chromosome Location	chr4:79430572-79430573
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78976661..78978805-chr4:79430192..79432122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138759	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10001606	0.94[ASN][1000 genomes]
rs10004305	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10006660	0.95[ASN][1000 genomes]
rs10020703	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10028215	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10028729	0.95[ASN][1000 genomes]
rs10030160	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10030186	0.94[ASN][1000 genomes]
rs10030467	0.94[ASN][1000 genomes]
rs10030759	0.95[ASN][1000 genomes]
rs10033081	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10033137	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1027447	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1027449	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727770	0.99[ASN][1000 genomes]
rs11730025	0.97[ASN][1000 genomes]
rs12332067	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13107007	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13108822	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13111617	0.99[ASN][1000 genomes]
rs13118276	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132231	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13141571	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13143325	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13435277	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1390747	0.95[ASN][1000 genomes]
rs1496585	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496586	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496587	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496588	0.97[ASN][1000 genomes]
rs1496598	0.94[ASN][1000 genomes]
rs1496607	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1542823	0.94[ASN][1000 genomes]
rs17003289	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17003293	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17003294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17470289	0.97[ASN][1000 genomes]
rs28361383	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28449192	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28473345	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28488385	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28494791	0.99[ASN][1000 genomes]
rs28505110	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28545653	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28570979	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28651081	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867449	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2867450	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867451	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867452	0.83[ASN][1000 genomes]
rs2867453	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2867454	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28704649	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28721400	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28725393	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28739412	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35150477	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35520641	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35702927	0.99[ASN][1000 genomes]
rs3749488	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762843	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792608	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453958	0.95[ASN][1000 genomes]
rs55744800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59249633	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59857077	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60285643	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60438529	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60520656	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62310262	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310263	0.83[ASN][1000 genomes]
rs62310266	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310267	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62310269	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310270	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310271	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62310273	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310274	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310275	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310307	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62310308	0.92[ASN][1000 genomes]
rs62310309	0.92[ASN][1000 genomes]
rs62310310	0.91[ASN][1000 genomes]
rs6533730	0.97[ASN][1000 genomes]
rs67201837	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67217470	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67993554	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829018	0.94[ASN][1000 genomes]
rs6844368	0.94[ASN][1000 genomes]
rs71611022	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7669587	0.94[ASN][1000 genomes]
rs7674053	0.81[EUR][1000 genomes]
rs7675424	0.97[ASN][1000 genomes]
rs7696362	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697796	0.94[ASN][1000 genomes]
rs931606	0.94[ASN][1000 genomes]
rs9685861	0.94[ASN][1000 genomes]
rs9990780	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9996383	0.94[ASN][1000 genomes]
rs9997583	0.94[ASN][1000 genomes]
rs9999496	0.95[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	esv10951	chr4:79421607-79431447	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
5	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
6	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
8	chr4:79403200-79449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:79404200-79450200	Weak transcription	HMEC	breast
10	chr4:79404400-79431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:79408600-79435000	Weak transcription	Fetal Heart	heart
12	chr4:79410200-79443600	Weak transcription	HSMMtube	muscle
13	chr4:79410200-79461800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:79410800-79439800	Weak transcription	Fetal Lung	lung
15	chr4:79418000-79437800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:79418200-79431200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:79420400-79445000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:79421800-79445200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:79426800-79455000	Weak transcription	Esophagus	oesophagus
20	chr4:79427200-79430800	Strong transcription	Fetal Intestine Small	intestine
21	chr4:79427600-79435200	Weak transcription	Fetal Stomach	stomach
22	chr4:79427800-79439400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:79428000-79430600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:79428000-79430800	Strong transcription	Fetal Intestine Large	intestine
25	chr4:79428000-79432200	Strong transcription	HepG2	liver
26	chr4:79428000-79432600	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr4:79428000-79437400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr4:79428000-79437400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:79428000-79438400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:79428200-79466200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:79428400-79437400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:79428600-79431000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:79428600-79432000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr4:79428600-79437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:79428600-79449800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:79428600-79459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:79428800-79430800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:79429400-79434800	Weak transcription	Fetal Kidney	kidney
39	chr4:79429800-79430800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:79429800-79431000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:79430200-79432000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:79430200-79432400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:79430200-79439800	Weak transcription	Left Ventricle	heart
44	chr4:79430200-79456000	Weak transcription	Aorta	Aorta
45	chr4:79430200-79456000	Weak transcription	Pancreas	Pancrea

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