Variant report

Variant	rs28610339
Chromosome Location	chr5:60712747-60712748
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60711785..60713945-chr5:60718973..60721238,2	K562	blood:
2	chr5:60704554..60708458-chr5:60711463..60715174,4	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10041978	0.87[ASN][1000 genomes]
rs1045352	0.88[AMR][1000 genomes]
rs10939900	0.99[ASN][1000 genomes]
rs10939901	0.99[ASN][1000 genomes]
rs10939902	1.00[ASN][1000 genomes]
rs10939903	0.87[ASN][1000 genomes]
rs10939905	0.90[AMR][1000 genomes]
rs11742658	0.90[AMR][1000 genomes]
rs11743711	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11747564	0.90[AMR][1000 genomes]
rs11749200	0.88[AMR][1000 genomes]
rs11750589	0.98[ASN][1000 genomes]
rs11950318	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11952146	0.88[AMR][1000 genomes]
rs11954430	0.81[ASN][1000 genomes]
rs12187112	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188627	0.94[ASN][1000 genomes]
rs12189001	0.99[ASN][1000 genomes]
rs12518479	0.99[ASN][1000 genomes]
rs12520628	0.99[ASN][1000 genomes]
rs12522647	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13156100	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13157657	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13157831	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13158675	0.99[ASN][1000 genomes]
rs13159018	0.89[AMR][1000 genomes]
rs13159166	0.86[AMR][1000 genomes]
rs13160801	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13162358	0.99[ASN][1000 genomes]
rs13162694	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163970	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13166934	0.88[AMR][1000 genomes]
rs13169711	0.99[ASN][1000 genomes]
rs13170135	0.96[ASN][1000 genomes]
rs13170262	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13171497	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13171757	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172080	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13172084	0.86[AMR][1000 genomes]
rs13178686	0.99[ASN][1000 genomes]
rs13179091	0.88[AMR][1000 genomes]
rs13179617	0.85[AMR][1000 genomes]
rs13181015	0.98[ASN][1000 genomes]
rs13185783	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13186194	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13188327	0.92[ASN][1000 genomes]
rs13188685	0.88[AMR][1000 genomes]
rs1348716	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1363892	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1374043	0.81[ASN][1000 genomes]
rs1445979	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445980	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1445981	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1477355	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986252	0.81[ASN][1000 genomes]
rs2034239	0.87[AMR][1000 genomes]
rs2053693	0.89[AMR][1000 genomes]
rs2276987	0.87[AMR][1000 genomes]
rs34739794	0.96[ASN][1000 genomes]
rs35262187	0.99[ASN][1000 genomes]
rs4276369	0.94[ASN][1000 genomes]
rs4392578	0.99[ASN][1000 genomes]
rs4484384	0.99[ASN][1000 genomes]
rs4604142	0.99[ASN][1000 genomes]
rs5027472	0.90[ASN][1000 genomes]
rs55838118	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56035042	0.99[ASN][1000 genomes]
rs60529601	0.99[ASN][1000 genomes]
rs60886975	0.99[ASN][1000 genomes]
rs62368660	0.99[ASN][1000 genomes]
rs6449528	0.99[ASN][1000 genomes]
rs6449529	0.99[ASN][1000 genomes]
rs6449530	0.98[ASN][1000 genomes]
rs6449531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449533	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449535	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6860608	0.98[ASN][1000 genomes]
rs6865624	0.89[AMR][1000 genomes]
rs6873712	0.89[AMR][1000 genomes]
rs6874264	0.89[AMR][1000 genomes]
rs6874266	0.89[AMR][1000 genomes]
rs6877610	0.99[ASN][1000 genomes]
rs6878927	0.89[AMR][1000 genomes]
rs6881765	0.99[ASN][1000 genomes]
rs6881799	0.89[AMR][1000 genomes]
rs6882136	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6885005	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890351	0.88[AMR][1000 genomes]
rs6894675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895046	0.81[ASN][1000 genomes]
rs7443602	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7700289	0.99[ASN][1000 genomes]
rs7701440	0.94[ASN][1000 genomes]
rs7709645	1.00[ASN][1000 genomes]
rs7714457	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714712	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717082	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7719647	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7722810	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7724551	0.96[ASN][1000 genomes]
rs7727824	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734879	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60698000-60725400	Weak transcription	Spleen	Spleen
2	chr5:60705200-60727200	Weak transcription	Fetal Stomach	stomach
3	chr5:60705400-60713400	Weak transcription	Brain Germinal Matrix	brain
4	chr5:60705400-60713600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:60705600-60719000	Weak transcription	Fetal Brain Male	brain
6	chr5:60706000-60713400	Weak transcription	Adipose Nuclei	Adipose
7	chr5:60706000-60713600	Weak transcription	Primary B cells from cord blood	blood
8	chr5:60706000-60719200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:60706000-60721400	Weak transcription	Fetal Intestine Large	intestine
10	chr5:60706000-60728000	Weak transcription	Fetal Intestine Small	intestine
11	chr5:60706200-60719400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:60706200-60727800	Weak transcription	HUVEC	blood vessel
13	chr5:60708400-60713400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:60708400-60719200	Weak transcription	Ovary	ovary
15	chr5:60709800-60712800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:60709800-60713200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr5:60709800-60713800	Enhancers	Brain Substantia Nigra	brain
18	chr5:60709800-60714000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:60709800-60714000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:60709800-60714000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:60709800-60714000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:60709800-60714000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr5:60709800-60714000	Enhancers	Brain Anterior Caudate	brain
24	chr5:60709800-60716400	Enhancers	Brain Hippocampus Middle	brain
25	chr5:60710000-60719200	Weak transcription	NHLF	lung
26	chr5:60710200-60719600	Weak transcription	Left Ventricle	heart
27	chr5:60710600-60714000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:60710800-60712800	Enhancers	NHEK	skin
29	chr5:60711000-60719400	Weak transcription	Psoas Muscle	Psoas
30	chr5:60711000-60735800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:60711200-60713200	Weak transcription	Stomach Mucosa	stomach
32	chr5:60711200-60713600	Enhancers	Colon Smooth Muscle	Colon
33	chr5:60711200-60713800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:60711400-60713600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr5:60711400-60714000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:60711400-60714000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:60711600-60712800	Enhancers	HMEC	breast
38	chr5:60711600-60714000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:60711600-60714000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:60711800-60712800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr5:60711800-60712800	Enhancers	Fetal Heart	heart
42	chr5:60711800-60712800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr5:60711800-60712800	Enhancers	NH-A	brain
44	chr5:60711800-60713400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:60711800-60713800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:60711800-60713800	Enhancers	Fetal Lung	lung
47	chr5:60711800-60714000	Enhancers	Brain Cingulate Gyrus	brain
48	chr5:60711800-60716400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:60712000-60712800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:60712000-60713800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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