Variant report

Variant	rs7727824
Chromosome Location	chr5:60706426-60706427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60704554..60708458-chr5:60711463..60715174,4	MCF-7	breast:
2	chr5:60456910..60459732-chr5:60703515..60707130,5	MCF-7	breast:
3	chr5:60626312..60629944-chr5:60702524..60707105,7	MCF-7	breast:
4	chr5:60703951..60706510-chr5:60708254..60709801,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction

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	0.81[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	0.81[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	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	0.94[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	0.90[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	0.96[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	0.93[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	0.93[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]
rs28610339	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449533	0.82[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	0.87[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	0.95[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	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]
rs7734879	0.92[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:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60682000-60709800	Weak transcription	Left Ventricle	heart
2	chr5:60682600-60712400	Weak transcription	Esophagus	oesophagus
3	chr5:60687600-60711800	Weak transcription	Aorta	Aorta
4	chr5:60690800-60706800	Weak transcription	Gastric	stomach
5	chr5:60698000-60725400	Weak transcription	Spleen	Spleen
6	chr5:60699400-60706800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:60703600-60708800	Enhancers	Brain Substantia Nigra	brain
8	chr5:60704800-60706800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:60704800-60708400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr5:60704800-60709800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:60704800-60709800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:60704800-60709800	Weak transcription	Pancreas	Pancrea
13	chr5:60705000-60707800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:60705000-60708200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:60705200-60707200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:60705200-60708000	Weak transcription	Ovary	ovary
17	chr5:60705200-60708200	Enhancers	Brain Anterior Caudate	brain
18	chr5:60705200-60708600	Enhancers	Brain Hippocampus Middle	brain
19	chr5:60705200-60727200	Weak transcription	Fetal Stomach	stomach
20	chr5:60705400-60707200	Enhancers	NH-A	brain
21	chr5:60705400-60708000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:60705400-60708400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:60705400-60708400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:60705400-60713400	Weak transcription	Brain Germinal Matrix	brain
25	chr5:60705400-60713600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:60705600-60706800	Weak transcription	Fetal Lung	lung
27	chr5:60705600-60712200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:60705600-60719000	Weak transcription	Fetal Brain Male	brain
29	chr5:60705800-60706800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:60705800-60707000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:60705800-60707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:60705800-60707400	Weak transcription	Fetal Brain Female	brain
33	chr5:60705800-60707600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:60705800-60708400	Enhancers	Brain Cingulate Gyrus	brain
35	chr5:60705800-60708600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:60705800-60709800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:60705800-60709800	Weak transcription	Liver	Liver
38	chr5:60705800-60710400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:60705800-60711400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:60706000-60706600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:60706000-60707000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:60706000-60707000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:60706000-60707000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr5:60706000-60707400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:60706000-60707400	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:60706000-60707800	Weak transcription	Brain Angular Gyrus	brain
47	chr5:60706000-60708000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:60706000-60709800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:60706000-60709800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:60706000-60709800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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