Variant report

Variant	rs7230461
Chromosome Location	chr18:28823765-28823766
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	chr18:28680633..28683180-chr18:28821248..28824915,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134755	Chromatin interaction
ENSG00000265888	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11659665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11660638	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11663924	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11664596	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11873223	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11873281	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12606446	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12606722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12957659	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12958069	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12958073	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12958351	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12958377	0.86[EUR][1000 genomes]
rs12959058	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12964422	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12964443	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12964744	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12964748	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12964839	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12964907	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12965148	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12965177	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12965803	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12965829	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1544880	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1593511	0.82[EUR][1000 genomes]
rs17658464	0.91[EUR][1000 genomes]
rs2042720	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162274	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28372393	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28510667	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28615832	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28633353	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34187983	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34212801	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34301793	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34530511	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34634416	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34664857	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34743470	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35136508	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35220971	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35223713	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35229932	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35257713	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35287825	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35362621	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35596545	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35909227	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4349226	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4408611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4517864	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4539673	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4598984	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55776955	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55778425	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55965644	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56088904	0.88[EUR][1000 genomes]
rs56308568	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62087700	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62087701	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62087702	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62087703	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62088665	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62090396	0.84[EUR][1000 genomes]
rs62090401	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6506899	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6506903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6506904	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67014182	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67550130	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7226461	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227412	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7229569	0.82[EUR][1000 genomes]
rs7231460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7232206	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7235384	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239695	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7240897	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7241874	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7242742	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243151	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7243262	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7243638	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7243885	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7243922	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7243984	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7244015	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7244050	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7244153	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7244510	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7245008	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72914749	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8087103	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8087786	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8088637	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8088973	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089598	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8089762	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8091715	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091871	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9946611	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9950769	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9950949	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9950971	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9951016	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9951341	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9957758	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9963626	0.84[AMR][1000 genomes];0.95[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	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28820200-28826000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr18:28820400-28823800	Enhancers	HepG2	liver
3	chr18:28820400-28824800	Enhancers	HMEC	breast
4	chr18:28820600-28824600	Enhancers	Fetal Intestine Large	intestine
5	chr18:28820600-28824600	Enhancers	Fetal Intestine Small	intestine
6	chr18:28820600-28828000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr18:28820800-28826200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr18:28821200-28823800	Enhancers	Liver	Liver
9	chr18:28821200-28824800	Enhancers	Stomach Mucosa	stomach
10	chr18:28821200-28826000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr18:28821400-28823800	Weak transcription	Pancreas	Pancrea
12	chr18:28821400-28823800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr18:28821400-28824800	Enhancers	Fetal Kidney	kidney
14	chr18:28821400-28825200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:28821600-28823800	Weak transcription	Small Intestine	intestine
16	chr18:28822000-28824000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr18:28822200-28823800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:28822200-28823800	Weak transcription	Placenta	Placenta
19	chr18:28822200-28824400	Weak transcription	NH-A	brain
20	chr18:28822200-28824600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:28822200-28826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:28822400-28823800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:28822400-28824000	Enhancers	A549	lung
24	chr18:28822400-28824600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr18:28822600-28823800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr18:28822600-28823800	Enhancers	Duodenum Mucosa	Duodenum
27	chr18:28822600-28823800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr18:28822600-28823800	Enhancers	NHEK	skin
29	chr18:28822600-28824600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:28822800-28823800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr18:28822800-28823800	Weak transcription	Hela-S3	cervix
32	chr18:28822800-28824200	Weak transcription	Fetal Lung	lung
33	chr18:28822800-28824600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr18:28823000-28823800	Enhancers	HUVEC	blood vessel
35	chr18:28823000-28824000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr18:28823200-28826000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr18:28823600-28823800	Weak transcription	Colonic Mucosa	Colon
38	chr18:28823600-28823800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr18:28823600-28824200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr18:28823600-28824600	Enhancers	GM12878-XiMat	blood
41	chr18:28823600-28824800	Enhancers	Left Ventricle	heart
42	chr18:28823600-28825000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr18:28823600-28825000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr18:28823600-28825200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr18:28823600-28825400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:28823600-28825400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr18:28823600-28825400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr18:28823600-28825800	Enhancers	HUES48 Cell Line	embryonic stem cell

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