Variant report

Variant	rs9625416
Chromosome Location	chr22:28543800-28543801
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	chr22:28539281..28541367-chr22:28542040..28544765,2	MCF-7	breast:

Extended variants
information (count: 167 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs10154425	0.89[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10212007	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10212036	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10212040	0.87[AMR][1000 genomes]
rs10212074	0.89[AMR][1000 genomes]
rs10212083	0.82[CEU][hapmap]
rs10483140	0.86[EUR][1000 genomes]
rs10483142	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10483143	0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs118840	0.89[EUR][1000 genomes]
rs12165651	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12165797	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12166023	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12166077	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs12166158	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12166164	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12166256	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12166389	0.88[EUR][1000 genomes]
rs12166719	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12166740	1.00[CEU][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs12166912	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12166938	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12167320	0.88[EUR][1000 genomes]
rs12167735	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12167829	0.88[EUR][1000 genomes]
rs12168054	0.89[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12168180	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12168251	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12168582	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12168652	0.81[EUR][1000 genomes]
rs12169097	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12169888	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12169936	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12170022	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12170558	0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12170953	0.89[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12171104	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs134194	0.81[CEU][hapmap]
rs138636	0.89[EUR][1000 genomes]
rs138637	0.89[EUR][1000 genomes]
rs138639	0.89[EUR][1000 genomes]
rs138640	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs138642	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs138651	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs138653	0.89[CEU][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes]
rs138654	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138655	0.95[EUR][1000 genomes]
rs138656	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138658	0.89[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs138660	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138664	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138665	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138667	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138669	0.87[EUR][1000 genomes]
rs138670	0.89[EUR][1000 genomes]
rs138671	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs138672	0.95[EUR][1000 genomes]
rs16985763	0.88[EUR][1000 genomes]
rs16985967	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16985976	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16986037	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16986077	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16987005	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17390800	0.88[EUR][1000 genomes]
rs17407024	0.88[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17483887	0.89[CEU][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes]
rs17484337	0.89[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2143420	0.89[YRI][hapmap]
rs2345717	1.00[ASN][1000 genomes]
rs2745562	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28375646	0.95[EUR][1000 genomes]
rs28579300	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4036493	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs470098	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs470102	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs470103	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs470104	0.95[EUR][1000 genomes]
rs55846737	1.00[ASN][1000 genomes]
rs55856549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56233401	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56393679	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57686964	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58050941	0.89[EUR][1000 genomes]
rs58823697	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7286519	0.95[EUR][1000 genomes]
rs7288331	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7289984	0.88[EUR][1000 genomes]
rs7292562	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73880355	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73880374	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880375	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880376	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880381	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73880382	0.87[EUR][1000 genomes]
rs73880383	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73880384	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73880385	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73880387	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73880393	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73880395	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73880398	0.84[AFR][1000 genomes]
rs73882704	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73882705	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73882709	0.81[EUR][1000 genomes]
rs761322	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs761323	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8141163	0.88[EUR][1000 genomes]
rs8141173	0.88[EUR][1000 genomes]
rs9306451	0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9306452	0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9620752	0.88[EUR][1000 genomes]
rs9620753	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9620755	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9620757	0.88[EUR][1000 genomes]
rs9620762	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9620764	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620766	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9620767	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9620768	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620769	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620770	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9620771	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620778	0.81[CEU][hapmap]
rs9620779	0.82[CEU][hapmap]
rs9625361	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625363	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625366	0.86[EUR][1000 genomes]
rs9625367	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625370	0.88[EUR][1000 genomes]
rs9625374	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625375	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625377	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625387	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9625388	0.95[EUR][1000 genomes]
rs9625390	0.89[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625391	0.89[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625393	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625395	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9625396	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625397	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625398	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625399	0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625400	0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625402	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625403	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625405	0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9625406	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9625407	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625408	0.89[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9625409	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625410	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9625413	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9625415	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625425	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625427	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625430	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625437	0.82[CEU][hapmap]
rs9625447	1.00[ASN][1000 genomes]
rs9712839	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs988893	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9985213	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28533800-28559000	Weak transcription	Aorta	Aorta
2	chr22:28534200-28545200	Enhancers	Fetal Lung	lung
3	chr22:28534400-28544000	Enhancers	Fetal Brain Male	brain
4	chr22:28536000-28544400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:28536200-28546600	Weak transcription	Left Ventricle	heart
6	chr22:28536200-28549600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr22:28536800-28543800	Enhancers	Fetal Brain Female	brain
8	chr22:28537200-28558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr22:28538400-28544800	Weak transcription	Dnd41	blood
10	chr22:28538800-28549800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr22:28539200-28547000	Weak transcription	Fetal Intestine Small	intestine
12	chr22:28539200-28558400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr22:28539600-28549800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr22:28540200-28558600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr22:28540200-28567800	Weak transcription	Gastric	stomach
16	chr22:28540400-28550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:28540800-28546200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:28540800-28547400	Weak transcription	NHLF	lung
19	chr22:28540800-28549800	Weak transcription	Psoas Muscle	Psoas
20	chr22:28540800-28567800	Weak transcription	Small Intestine	intestine
21	chr22:28541000-28547200	Weak transcription	Right Atrium	heart
22	chr22:28541000-28553000	Weak transcription	Fetal Muscle Leg	muscle
23	chr22:28541000-28557200	Weak transcription	Lung	lung
24	chr22:28541800-28544000	Enhancers	Brain Substantia Nigra	brain
25	chr22:28542000-28543800	Enhancers	Brain Hippocampus Middle	brain
26	chr22:28542000-28543800	Enhancers	Fetal Stomach	stomach
27	chr22:28542000-28544200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:28542000-28544200	Enhancers	Brain Cingulate Gyrus	brain
29	chr22:28542200-28544000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:28542200-28544200	Enhancers	Brain Angular Gyrus	brain
31	chr22:28542200-28544400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr22:28542200-28544400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:28542400-28543800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:28542400-28544000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr22:28542600-28544000	Enhancers	HSMMtube	muscle
36	chr22:28542600-28546400	Weak transcription	HSMM	muscle
37	chr22:28542800-28543800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:28542800-28543800	Enhancers	Fetal Heart	heart
39	chr22:28542800-28543800	Enhancers	Osteobl	bone
40	chr22:28542800-28548000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr22:28543000-28546800	Weak transcription	Ovary	ovary
42	chr22:28543000-28549600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr22:28543200-28543800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:28543200-28544000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr22:28543200-28548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr22:28543200-28548200	Weak transcription	Right Ventricle	heart
47	chr22:28543400-28544200	Enhancers	Brain Anterior Caudate	brain
48	chr22:28543400-28546400	Weak transcription	Colon Smooth Muscle	Colon
49	chr22:28543400-28548200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr22:28543400-28548200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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