Variant report

Variant	rs138669
Chromosome Location	chr22:28408066-28408067
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28283009..28285381-chr22:28406270..28408539,2	MCF-7	breast:
2	chr22:28312284..28315668-chr22:28406606..28409523,3	MCF-7	breast:
3	chr22:28401393..28403661-chr22:28406646..28408733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180957	Chromatin interaction
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10154425	0.87[EUR][1000 genomes]
rs10483140	0.84[EUR][1000 genomes]
rs10483142	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483143	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs118840	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165651	0.86[EUR][1000 genomes]
rs12165797	0.86[EUR][1000 genomes]
rs12166023	0.86[EUR][1000 genomes]
rs12166077	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166158	0.87[EUR][1000 genomes]
rs12166256	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166389	0.86[EUR][1000 genomes]
rs12166719	1.00[ASN][1000 genomes]
rs12166740	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166912	0.87[EUR][1000 genomes]
rs12166938	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167320	0.86[EUR][1000 genomes]
rs12167829	0.86[EUR][1000 genomes]
rs12168054	0.89[EUR][1000 genomes]
rs12168180	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168251	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168582	0.84[EUR][1000 genomes]
rs12169097	0.86[EUR][1000 genomes]
rs12169888	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169936	0.86[EUR][1000 genomes]
rs12170022	0.87[EUR][1000 genomes]
rs12170558	1.00[ASN][1000 genomes]
rs12170953	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171104	0.84[EUR][1000 genomes]
rs138636	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138637	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138639	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138640	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138642	0.87[EUR][1000 genomes]
rs138651	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138653	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138654	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138655	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138656	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs138658	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138660	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138664	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138665	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138667	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138670	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs138671	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138672	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985763	0.86[EUR][1000 genomes]
rs16985967	1.00[ASN][1000 genomes]
rs16986037	0.87[EUR][1000 genomes]
rs16987005	0.87[EUR][1000 genomes]
rs17390800	0.86[EUR][1000 genomes]
rs17407024	0.83[EUR][1000 genomes]
rs17483887	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17484337	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745562	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375646	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470098	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470102	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470103	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470104	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55856549	0.82[EUR][1000 genomes]
rs56233401	0.87[EUR][1000 genomes]
rs56393679	1.00[ASN][1000 genomes]
rs57686964	0.87[EUR][1000 genomes]
rs58050941	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58823697	0.87[EUR][1000 genomes]
rs7286519	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288331	0.86[EUR][1000 genomes]
rs7289984	0.86[EUR][1000 genomes]
rs7292562	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880355	0.84[EUR][1000 genomes]
rs73880374	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880375	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880376	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880381	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880382	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880383	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880384	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880385	1.00[ASN][1000 genomes]
rs73880387	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880393	0.86[EUR][1000 genomes]
rs761323	0.87[EUR][1000 genomes]
rs8141163	0.86[EUR][1000 genomes]
rs8141173	0.86[EUR][1000 genomes]
rs9306451	1.00[ASN][1000 genomes]
rs9620752	0.86[EUR][1000 genomes]
rs9620753	0.86[EUR][1000 genomes]
rs9620755	0.83[EUR][1000 genomes]
rs9620757	0.86[EUR][1000 genomes]
rs9620762	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620764	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620766	1.00[ASN][1000 genomes]
rs9620767	1.00[ASN][1000 genomes]
rs9620768	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620769	0.86[EUR][1000 genomes]
rs9620771	0.86[EUR][1000 genomes]
rs9625361	0.84[EUR][1000 genomes]
rs9625363	0.86[EUR][1000 genomes]
rs9625366	0.84[EUR][1000 genomes]
rs9625367	0.86[EUR][1000 genomes]
rs9625370	0.86[EUR][1000 genomes]
rs9625374	0.86[EUR][1000 genomes]
rs9625375	0.86[EUR][1000 genomes]
rs9625377	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625387	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625388	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625390	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625391	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625393	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625395	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625396	1.00[ASN][1000 genomes]
rs9625397	1.00[ASN][1000 genomes]
rs9625398	1.00[ASN][1000 genomes]
rs9625399	1.00[ASN][1000 genomes]
rs9625400	1.00[ASN][1000 genomes]
rs9625402	1.00[ASN][1000 genomes]
rs9625403	1.00[ASN][1000 genomes]
rs9625406	0.92[EUR][1000 genomes]
rs9625407	0.90[EUR][1000 genomes]
rs9625408	0.87[EUR][1000 genomes]
rs9625409	0.86[EUR][1000 genomes]
rs9625410	0.84[EUR][1000 genomes]
rs9625413	0.87[EUR][1000 genomes]
rs9625415	0.92[EUR][1000 genomes]
rs9625416	0.87[EUR][1000 genomes]
rs9625417	0.87[EUR][1000 genomes]
rs9625418	0.86[EUR][1000 genomes]
rs9625421	0.82[EUR][1000 genomes]
rs9625427	0.81[EUR][1000 genomes]
rs9625430	0.82[EUR][1000 genomes]
rs9712839	1.00[ASN][1000 genomes]
rs9985213	0.86[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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
7	chr22:28393400-28408800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:28394800-28414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr22:28395200-28409200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:28395400-28409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr22:28395600-28408200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
14	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
15	chr22:28397200-28409400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr22:28397200-28423000	Weak transcription	HepG2	liver
17	chr22:28397400-28408800	Weak transcription	Brain Angular Gyrus	brain
18	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
19	chr22:28399400-28425800	Weak transcription	Liver	Liver
20	chr22:28399600-28409000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr22:28400800-28410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr22:28401600-28409000	Strong transcription	Fetal Muscle Leg	muscle
23	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
24	chr22:28401800-28408200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr22:28401800-28410400	Weak transcription	Fetal Thymus	thymus
26	chr22:28402400-28409600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr22:28405200-28408200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:28405200-28414000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:28405400-28408200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr22:28405400-28408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr22:28405400-28408200	Weak transcription	Fetal Lung	lung
32	chr22:28405400-28408800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:28405400-28412400	Weak transcription	Brain Hippocampus Middle	brain
34	chr22:28405400-28415000	Weak transcription	HSMM	muscle
35	chr22:28405400-28416200	Weak transcription	NHDF-Ad	bronchial
36	chr22:28405400-28416200	Weak transcription	NHLF	lung
37	chr22:28405400-28416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr22:28405400-28416400	Weak transcription	Fetal Kidney	kidney
39	chr22:28405600-28412400	Weak transcription	Brain Anterior Caudate	brain
40	chr22:28405600-28414800	Weak transcription	HSMMtube	muscle
41	chr22:28405800-28408200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr22:28405800-28409200	Weak transcription	Brain Substantia Nigra	brain
43	chr22:28405800-28409400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr22:28405800-28410000	Weak transcription	Fetal Brain Male	brain
45	chr22:28405800-28411400	Strong transcription	Fetal Intestine Small	intestine
46	chr22:28405800-28414000	Weak transcription	Psoas Muscle	Psoas
47	chr22:28405800-28416000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr22:28405800-28416200	Weak transcription	Left Ventricle	heart
49	chr22:28406200-28409800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:28406200-28410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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