Variant report

Variant	rs138670
Chromosome Location	chr22:28408313-28408314
allele	C/T
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: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10154425	0.89[EUR][1000 genomes]
rs10212036	0.81[EUR][1000 genomes]
rs10483140	0.86[EUR][1000 genomes]
rs10483142	0.84[EUR][1000 genomes]
rs10483143	0.84[EUR][1000 genomes]
rs118840	0.89[EUR][1000 genomes]
rs12165651	0.88[EUR][1000 genomes]
rs12165797	0.88[EUR][1000 genomes]
rs12166023	0.88[EUR][1000 genomes]
rs12166077	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12166158	0.89[EUR][1000 genomes]
rs12166164	0.81[EUR][1000 genomes]
rs12166256	0.89[EUR][1000 genomes]
rs12166389	0.88[EUR][1000 genomes]
rs12166719	0.81[EUR][1000 genomes]
rs12166740	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12166912	0.89[EUR][1000 genomes]
rs12166938	0.84[EUR][1000 genomes]
rs12167320	0.88[EUR][1000 genomes]
rs12167829	0.88[EUR][1000 genomes]
rs12168054	0.91[EUR][1000 genomes]
rs12168180	0.88[EUR][1000 genomes]
rs12168251	0.84[EUR][1000 genomes]
rs12168582	0.86[EUR][1000 genomes]
rs12169097	0.88[EUR][1000 genomes]
rs12169888	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12169936	0.88[EUR][1000 genomes]
rs12170022	0.89[EUR][1000 genomes]
rs12170558	0.82[EUR][1000 genomes]
rs12170953	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12171104	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs138636	0.89[EUR][1000 genomes]
rs138637	0.89[EUR][1000 genomes]
rs138639	0.89[EUR][1000 genomes]
rs138640	0.89[EUR][1000 genomes]
rs138642	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs138651	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138653	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs138654	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138655	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138658	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138660	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138664	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138665	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138667	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138669	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs138671	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138672	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16985763	0.88[EUR][1000 genomes]
rs16985967	0.81[EUR][1000 genomes]
rs16985976	0.81[EUR][1000 genomes]
rs16986037	0.89[EUR][1000 genomes]
rs16986077	0.81[EUR][1000 genomes]
rs16987005	0.89[EUR][1000 genomes]
rs17390800	0.88[EUR][1000 genomes]
rs17407024	0.86[EUR][1000 genomes]
rs17483887	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17484337	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2745562	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28375646	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470098	0.89[EUR][1000 genomes]
rs470102	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470103	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470104	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55856549	0.84[EUR][1000 genomes]
rs56233401	0.89[EUR][1000 genomes]
rs56393679	0.81[EUR][1000 genomes]
rs57686964	0.89[EUR][1000 genomes]
rs58050941	0.89[EUR][1000 genomes]
rs58823697	0.89[EUR][1000 genomes]
rs7286519	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7288331	0.88[EUR][1000 genomes]
rs7289984	0.88[EUR][1000 genomes]
rs7292562	0.88[EUR][1000 genomes]
rs73880355	0.86[EUR][1000 genomes]
rs73880374	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880375	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880376	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880381	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880382	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73880383	0.84[EUR][1000 genomes]
rs73880384	0.84[EUR][1000 genomes]
rs73880385	0.82[EUR][1000 genomes]
rs73880387	0.91[EUR][1000 genomes]
rs73880393	0.88[EUR][1000 genomes]
rs73880395	0.81[EUR][1000 genomes]
rs761322	0.82[EUR][1000 genomes]
rs761323	0.89[EUR][1000 genomes]
rs8141163	0.88[EUR][1000 genomes]
rs8141173	0.88[EUR][1000 genomes]
rs9306451	0.82[EUR][1000 genomes]
rs9306452	0.81[EUR][1000 genomes]
rs9620752	0.88[EUR][1000 genomes]
rs9620753	0.88[EUR][1000 genomes]
rs9620755	0.85[EUR][1000 genomes]
rs9620757	0.88[EUR][1000 genomes]
rs9620762	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620764	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620766	0.82[EUR][1000 genomes]
rs9620767	0.82[EUR][1000 genomes]
rs9620768	0.88[EUR][1000 genomes]
rs9620769	0.88[EUR][1000 genomes]
rs9620770	0.81[EUR][1000 genomes]
rs9620771	0.88[EUR][1000 genomes]
rs9625361	0.86[EUR][1000 genomes]
rs9625363	0.88[EUR][1000 genomes]
rs9625366	0.86[EUR][1000 genomes]
rs9625367	0.88[EUR][1000 genomes]
rs9625370	0.88[EUR][1000 genomes]
rs9625374	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9625375	0.88[EUR][1000 genomes]
rs9625377	0.88[EUR][1000 genomes]
rs9625387	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625388	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625390	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625391	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625393	0.84[EUR][1000 genomes]
rs9625395	0.89[EUR][1000 genomes]
rs9625396	0.82[EUR][1000 genomes]
rs9625397	0.82[EUR][1000 genomes]
rs9625398	0.82[EUR][1000 genomes]
rs9625399	0.82[EUR][1000 genomes]
rs9625400	0.82[EUR][1000 genomes]
rs9625402	0.82[EUR][1000 genomes]
rs9625403	0.81[EUR][1000 genomes]
rs9625405	0.81[EUR][1000 genomes]
rs9625406	0.80[EUR][1000 genomes]
rs9625408	0.89[EUR][1000 genomes]
rs9625409	0.88[EUR][1000 genomes]
rs9625410	0.86[EUR][1000 genomes]
rs9625413	0.89[EUR][1000 genomes]
rs9625415	0.88[EUR][1000 genomes]
rs9625416	0.89[EUR][1000 genomes]
rs9625417	0.89[EUR][1000 genomes]
rs9625418	0.88[EUR][1000 genomes]
rs9625421	0.84[EUR][1000 genomes]
rs9625430	0.81[EUR][1000 genomes]
rs9712839	0.81[EUR][1000 genomes]
rs9985213	0.88[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	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
13	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
14	chr22:28397200-28409400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr22:28397200-28423000	Weak transcription	HepG2	liver
16	chr22:28397400-28408800	Weak transcription	Brain Angular Gyrus	brain
17	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
18	chr22:28399400-28425800	Weak transcription	Liver	Liver
19	chr22:28399600-28409000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr22:28400800-28410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:28401600-28409000	Strong transcription	Fetal Muscle Leg	muscle
22	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
23	chr22:28401800-28410400	Weak transcription	Fetal Thymus	thymus
24	chr22:28402400-28409600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr22:28405200-28414000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr22:28405400-28408800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr22:28405400-28412400	Weak transcription	Brain Hippocampus Middle	brain
28	chr22:28405400-28415000	Weak transcription	HSMM	muscle
29	chr22:28405400-28416200	Weak transcription	NHDF-Ad	bronchial
30	chr22:28405400-28416200	Weak transcription	NHLF	lung
31	chr22:28405400-28416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr22:28405400-28416400	Weak transcription	Fetal Kidney	kidney
33	chr22:28405600-28412400	Weak transcription	Brain Anterior Caudate	brain
34	chr22:28405600-28414800	Weak transcription	HSMMtube	muscle
35	chr22:28405800-28409200	Weak transcription	Brain Substantia Nigra	brain
36	chr22:28405800-28409400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr22:28405800-28410000	Weak transcription	Fetal Brain Male	brain
38	chr22:28405800-28411400	Strong transcription	Fetal Intestine Small	intestine
39	chr22:28405800-28414000	Weak transcription	Psoas Muscle	Psoas
40	chr22:28405800-28416000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr22:28405800-28416200	Weak transcription	Left Ventricle	heart
42	chr22:28406200-28409800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:28406200-28410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr22:28406200-28411200	Strong transcription	Fetal Stomach	stomach
45	chr22:28406600-28410600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr22:28406800-28411000	Strong transcription	Ovary	ovary
47	chr22:28406800-28411800	Weak transcription	Fetal Heart	heart
48	chr22:28407000-28408800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr22:28407000-28409000	Weak transcription	Spleen	Spleen
50	chr22:28407000-28409200	Weak transcription	Esophagus	oesophagus

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