Variant report

Variant	rs28375646
Chromosome Location	chr22:28415314-28415315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:25042188..25043157-chr22:28415103..28415934,2	MCF-7	breast:

Extended variants
information (count: 150 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10154425	0.95[EUR][1000 genomes]
rs10212007	0.84[EUR][1000 genomes]
rs10212036	0.86[EUR][1000 genomes]
rs10483140	0.91[EUR][1000 genomes]
rs10483142	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483143	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs118840	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165651	0.93[EUR][1000 genomes]
rs12165797	0.93[EUR][1000 genomes]
rs12166023	0.93[EUR][1000 genomes]
rs12166077	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166158	0.95[EUR][1000 genomes]
rs12166164	0.86[EUR][1000 genomes]
rs12166256	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166389	0.93[EUR][1000 genomes]
rs12166719	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166740	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166912	0.95[EUR][1000 genomes]
rs12166938	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167320	0.93[EUR][1000 genomes]
rs12167829	0.93[EUR][1000 genomes]
rs12168054	0.96[EUR][1000 genomes]
rs12168180	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168251	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168582	0.91[EUR][1000 genomes]
rs12169097	0.93[EUR][1000 genomes]
rs12169888	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169936	0.93[EUR][1000 genomes]
rs12170022	0.95[EUR][1000 genomes]
rs12170558	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170953	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171104	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs138636	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138637	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138639	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138640	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138642	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138653	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138655	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138660	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138664	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138665	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138667	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138669	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138670	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985763	0.93[EUR][1000 genomes]
rs16985967	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985976	0.86[EUR][1000 genomes]
rs16986037	0.95[EUR][1000 genomes]
rs16986077	0.86[EUR][1000 genomes]
rs16987005	0.95[EUR][1000 genomes]
rs17390800	0.93[EUR][1000 genomes]
rs17407024	0.91[EUR][1000 genomes]
rs17483887	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17484337	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745562	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28579300	0.82[EUR][1000 genomes]
rs4036493	0.84[EUR][1000 genomes]
rs470098	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470102	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55856549	0.89[EUR][1000 genomes]
rs56233401	0.95[EUR][1000 genomes]
rs56393679	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57686964	0.95[EUR][1000 genomes]
rs58050941	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58823697	0.95[EUR][1000 genomes]
rs7286519	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288331	0.93[EUR][1000 genomes]
rs7289984	0.93[EUR][1000 genomes]
rs7292562	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880355	0.91[EUR][1000 genomes]
rs73880374	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880376	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880382	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880383	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880384	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880385	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880387	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880393	0.93[EUR][1000 genomes]
rs73880395	0.86[EUR][1000 genomes]
rs73882704	0.82[EUR][1000 genomes]
rs73882705	0.82[EUR][1000 genomes]
rs761322	0.87[EUR][1000 genomes]
rs761323	0.95[EUR][1000 genomes]
rs8141163	0.93[EUR][1000 genomes]
rs8141173	0.93[EUR][1000 genomes]
rs9306451	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306452	0.86[EUR][1000 genomes]
rs9620752	0.93[EUR][1000 genomes]
rs9620753	0.93[EUR][1000 genomes]
rs9620755	0.90[EUR][1000 genomes]
rs9620757	0.93[EUR][1000 genomes]
rs9620762	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620764	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620766	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620767	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620768	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620769	0.93[EUR][1000 genomes]
rs9620770	0.86[EUR][1000 genomes]
rs9620771	0.93[EUR][1000 genomes]
rs9625361	0.91[EUR][1000 genomes]
rs9625363	0.93[EUR][1000 genomes]
rs9625366	0.91[EUR][1000 genomes]
rs9625367	0.93[EUR][1000 genomes]
rs9625370	0.93[EUR][1000 genomes]
rs9625374	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9625375	0.93[EUR][1000 genomes]
rs9625377	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625390	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625391	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625393	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625395	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625396	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625397	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625398	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625399	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625400	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625402	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625403	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625405	0.86[EUR][1000 genomes]
rs9625406	0.85[EUR][1000 genomes]
rs9625407	0.84[EUR][1000 genomes]
rs9625408	0.95[EUR][1000 genomes]
rs9625409	0.93[EUR][1000 genomes]
rs9625410	0.91[EUR][1000 genomes]
rs9625413	0.95[EUR][1000 genomes]
rs9625415	0.93[EUR][1000 genomes]
rs9625416	0.95[EUR][1000 genomes]
rs9625417	0.95[EUR][1000 genomes]
rs9625418	0.93[EUR][1000 genomes]
rs9625421	0.89[EUR][1000 genomes]
rs9625425	0.82[EUR][1000 genomes]
rs9625427	0.84[EUR][1000 genomes]
rs9625430	0.86[EUR][1000 genomes]
rs9712839	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988893	0.82[EUR][1000 genomes]
rs9985213	0.93[EUR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
3	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
5	chr22:28397200-28423000	Weak transcription	HepG2	liver
6	chr22:28399400-28425800	Weak transcription	Liver	Liver
7	chr22:28405400-28416200	Weak transcription	NHDF-Ad	bronchial
8	chr22:28405400-28416200	Weak transcription	NHLF	lung
9	chr22:28405400-28416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr22:28405400-28416400	Weak transcription	Fetal Kidney	kidney
11	chr22:28405800-28416000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr22:28405800-28416200	Weak transcription	Left Ventricle	heart
13	chr22:28408800-28416200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr22:28409000-28428000	Genic enhancers	Fetal Muscle Leg	muscle
15	chr22:28409200-28416200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr22:28409400-28415800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr22:28409400-28430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr22:28409600-28416000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr22:28410000-28416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr22:28410200-28415800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr22:28410200-28416000	Weak transcription	Brain Substantia Nigra	brain
22	chr22:28410200-28423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr22:28410200-28423400	Weak transcription	Gastric	stomach
24	chr22:28410400-28415800	Weak transcription	Brain Angular Gyrus	brain
25	chr22:28410400-28416200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr22:28410400-28424200	Weak transcription	Aorta	Aorta
27	chr22:28411000-28416000	Weak transcription	Ovary	ovary
28	chr22:28411000-28423600	Weak transcription	Fetal Intestine Large	intestine
29	chr22:28411800-28418200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr22:28411800-28418400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr22:28412000-28416000	Strong transcription	Fetal Intestine Small	intestine
32	chr22:28412000-28418200	Enhancers	Right Ventricle	heart
33	chr22:28412400-28416000	Weak transcription	Colon Smooth Muscle	Colon
34	chr22:28412400-28416200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr22:28412400-28423000	Weak transcription	Adipose Nuclei	Adipose
36	chr22:28412600-28415800	Weak transcription	Placenta	Placenta
37	chr22:28412600-28415800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr22:28412600-28416000	Strong transcription	Fetal Stomach	stomach
39	chr22:28412600-28416200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:28412600-28416200	Weak transcription	Fetal Lung	lung
41	chr22:28412800-28416400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:28412800-28416400	Weak transcription	Fetal Brain Female	brain
43	chr22:28413200-28415800	Weak transcription	Lung	lung
44	chr22:28413200-28416000	Weak transcription	Brain Anterior Caudate	brain
45	chr22:28413200-28416000	Weak transcription	Pancreas	Pancrea
46	chr22:28413200-28416400	Weak transcription	Right Atrium	heart
47	chr22:28413800-28415600	Weak transcription	Brain Germinal Matrix	brain
48	chr22:28414000-28416400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:28414000-28416600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr22:28414200-28415600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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