Variant report

Variant	rs28493290
Chromosome Location	chr7:69113149-69113150
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:69112200..69113806-chr7:69119415..69121887,2	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1000874	0.93[EUR][1000 genomes]
rs10085600	0.97[EUR][1000 genomes]
rs10216097	0.97[EUR][1000 genomes]
rs10229336	0.87[EUR][1000 genomes]
rs10229578	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10229588	0.97[EUR][1000 genomes]
rs10230356	0.97[EUR][1000 genomes]
rs10230750	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10233869	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10234831	0.83[EUR][1000 genomes]
rs10236103	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10238307	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10239569	0.97[EUR][1000 genomes]
rs10240462	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10242206	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10243408	0.93[EUR][1000 genomes]
rs10244001	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10244128	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10244247	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10244885	0.93[EUR][1000 genomes]
rs10245493	0.81[ASN][1000 genomes]
rs10245690	0.97[EUR][1000 genomes]
rs10247386	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10248237	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10254086	0.97[EUR][1000 genomes]
rs10255563	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10255613	0.81[ASN][1000 genomes]
rs10256309	1.00[AMR][1000 genomes]
rs10256311	0.81[ASN][1000 genomes]
rs10256512	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10256943	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10257587	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10261380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10263467	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10268729	0.97[EUR][1000 genomes]
rs10269267	0.97[EUR][1000 genomes]
rs10272781	0.97[EUR][1000 genomes]
rs10274099	0.97[EUR][1000 genomes]
rs10274419	0.97[EUR][1000 genomes]
rs10275112	0.93[EUR][1000 genomes]
rs10275721	0.97[EUR][1000 genomes]
rs10276664	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10278978	0.97[EUR][1000 genomes]
rs10279669	0.97[EUR][1000 genomes]
rs10279708	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10280018	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10452705	0.97[EUR][1000 genomes]
rs10487943	0.97[EUR][1000 genomes]
rs10950193	0.85[EUR][1000 genomes]
rs11762049	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11764277	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11764717	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11769033	1.00[EUR][1000 genomes]
rs11769738	0.97[EUR][1000 genomes]
rs11770241	0.85[EUR][1000 genomes]
rs11771751	1.00[EUR][1000 genomes]
rs11771899	0.97[EUR][1000 genomes]
rs11772602	0.97[EUR][1000 genomes]
rs11975481	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11975506	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11979745	0.97[EUR][1000 genomes]
rs17140693	0.81[ASN][1000 genomes]
rs17140755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140783	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17140817	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17140884	0.97[EUR][1000 genomes]
rs17140938	0.97[EUR][1000 genomes]
rs17350805	0.80[EUR][1000 genomes]
rs17353920	0.87[EUR][1000 genomes]
rs17457910	0.87[EUR][1000 genomes]
rs17458713	0.87[EUR][1000 genomes]
rs2052124	0.87[EUR][1000 genomes]
rs2068718	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28524600	0.81[ASN][1000 genomes]
rs28577243	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2865804	0.93[EUR][1000 genomes]
rs28812289	0.97[EUR][1000 genomes]
rs34080361	0.93[EUR][1000 genomes]
rs3735260	0.85[ASN][1000 genomes]
rs3800979	0.93[EUR][1000 genomes]
rs41379648	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4305786	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55654955	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55693719	0.81[ASN][1000 genomes]
rs55756263	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55847506	0.81[ASN][1000 genomes]
rs55880824	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56800568	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57493471	0.97[EUR][1000 genomes]
rs58626042	0.97[EUR][1000 genomes]
rs58666988	0.93[EUR][1000 genomes]
rs58863846	0.97[EUR][1000 genomes]
rs61370051	0.85[EUR][1000 genomes]
rs61424317	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61692535	0.81[ASN][1000 genomes]
rs61744589	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62454937	0.81[ASN][1000 genomes]
rs62454938	0.81[ASN][1000 genomes]
rs6460525	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6945524	0.87[EUR][1000 genomes]
rs6947326	0.87[EUR][1000 genomes]
rs6950638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6951770	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6958450	0.93[EUR][1000 genomes]
rs6962237	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6962338	0.87[EUR][1000 genomes]
rs6967788	0.90[EUR][1000 genomes]
rs6975211	0.87[EUR][1000 genomes]
rs6977472	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6980305	0.80[EUR][1000 genomes]
rs717266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719294	0.93[EUR][1000 genomes]
rs73154605	0.97[EUR][1000 genomes]
rs73155227	0.81[ASN][1000 genomes]
rs73164795	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73166559	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73167506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73168739	0.93[EUR][1000 genomes]
rs73168740	0.97[EUR][1000 genomes]
rs73168747	0.87[EUR][1000 genomes]
rs73170834	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170857	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73170864	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73172903	0.90[EUR][1000 genomes]
rs7357113	0.81[ASN][1000 genomes]
rs740946	0.93[EUR][1000 genomes]
rs7777269	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7777621	0.93[EUR][1000 genomes]
rs7780835	0.97[EUR][1000 genomes]
rs7784950	0.97[EUR][1000 genomes]
rs7787342	0.81[ASN][1000 genomes]
rs7801209	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7810982	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs917718	0.87[EUR][1000 genomes]
rs917725	0.93[EUR][1000 genomes]
rs9690769	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69104600-69114200	Weak transcription	Brain Angular Gyrus	brain
2	chr7:69106200-69115600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:69106200-69119000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:69106200-69121600	Weak transcription	Fetal Kidney	kidney
5	chr7:69106400-69114000	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:69106400-69114200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:69107600-69113200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr7:69108200-69115600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:69108200-69118000	Weak transcription	Lung	lung
10	chr7:69109000-69115800	Weak transcription	Left Ventricle	heart
11	chr7:69109200-69115600	Weak transcription	Right Atrium	heart
12	chr7:69109200-69119000	Weak transcription	Fetal Stomach	stomach
13	chr7:69109400-69113800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:69109400-69118000	Weak transcription	Fetal Lung	lung
15	chr7:69109400-69119400	Weak transcription	Fetal Brain Female	brain
16	chr7:69109400-69121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:69109800-69119200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:69110000-69119400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:69110600-69117600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:69111000-69114000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:69111000-69115200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:69111000-69121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:69111200-69118000	Weak transcription	Adipose Nuclei	Adipose
24	chr7:69111400-69113800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr7:69112400-69114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:69112400-69114400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr7:69112600-69113200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:69112600-69113400	Enhancers	Brain Germinal Matrix	brain
29	chr7:69112600-69113600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr7:69112600-69114000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:69112600-69116200	Weak transcription	Fetal Intestine Small	intestine
32	chr7:69112600-69118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:69112600-69118000	Weak transcription	Psoas Muscle	Psoas
34	chr7:69112600-69118400	Weak transcription	Primary B cells from cord blood	blood
35	chr7:69112800-69115800	Weak transcription	GM12878-XiMat	blood
36	chr7:69112800-69116200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:69113000-69113600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:69113000-69115800	Weak transcription	Ovary	ovary
39	chr7:69113000-69118600	Weak transcription	Brain Anterior Caudate	brain
40	chr7:69113000-69118800	Weak transcription	Brain Hippocampus Middle	brain

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