Variant report

Variant	rs28625259
Chromosome Location	chr4:129095970-129095971
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	chr4:129093960..129096001-chr4:129097023..129099172,2	K562	blood:
2	chr4:129094288..129096291-chr4:129099385..129101465,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10000960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10001048	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10002580	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10014664	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1001503	0.87[EUR][1000 genomes]
rs10019554	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10019840	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10025430	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026899	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10213259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434053	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10518529	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1064205	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857128	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857129	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098946	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098950	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723915	0.87[EUR][1000 genomes]
rs11727049	0.91[EUR][1000 genomes]
rs11727305	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11728245	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732074	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735810	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737026	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11737508	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11941199	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498291	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12505717	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12506549	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12507742	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12508837	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509092	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12641548	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12645291	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12645577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648962	0.81[EUR][1000 genomes]
rs13102049	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109815	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13136665	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13138581	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13139182	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13139685	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1545711	0.87[EUR][1000 genomes]
rs16997980	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16997982	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1809796	0.83[AFR][1000 genomes]
rs1809797	0.83[AFR][1000 genomes]
rs1870686	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870687	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1908450	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1908451	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1961274	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1971933	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1975879	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1993722	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2056470	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2061570	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2061571	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2061572	0.84[EUR][1000 genomes]
rs2100798	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2100799	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2172813	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2204117	0.91[ASN][1000 genomes]
rs2306054	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306055	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2391231	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34021656	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34350456	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34503080	0.92[ASN][1000 genomes]
rs34658734	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34800130	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34816181	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34823354	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35239105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35636574	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733320	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4383632	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4493552	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4527494	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4541525	0.82[EUR][1000 genomes]
rs4576015	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4618332	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833394	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4833395	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4834226	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4834228	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4834229	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4834230	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834233	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834234	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975239	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55720227	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55849105	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55912890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57137613	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57492192	0.80[ASN][1000 genomes]
rs59944017	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62321076	0.90[ASN][1000 genomes]
rs62335638	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62335645	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62336165	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62336168	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6534659	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6534660	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534661	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6534662	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6534663	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6534666	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6534668	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6534669	0.98[ASN][1000 genomes]
rs6534670	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6534672	0.81[AFR][1000 genomes]
rs6534673	0.81[AFR][1000 genomes]
rs6811718	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6815163	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815890	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816751	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818467	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820515	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6820831	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829891	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834263	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6839370	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6842281	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849865	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6850479	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6851796	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6851896	0.89[ASN][1000 genomes]
rs6856312	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7661888	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7667562	0.83[AFR][1000 genomes]
rs7669406	0.90[ASN][1000 genomes]
rs7671235	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7671641	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7684955	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7691540	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691566	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692797	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7693135	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7696130	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9760909	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9760910	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9993435	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1792524	chr4:128983925-129133826	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv879929	chr4:129029653-129142079	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129067000-129107600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:129077400-129112600	Weak transcription	Left Ventricle	heart
3	chr4:129077400-129122000	Weak transcription	Aorta	Aorta
4	chr4:129077600-129103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:129077600-129120600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:129078000-129103400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:129078000-129107800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:129078000-129107800	Weak transcription	Fetal Stomach	stomach
9	chr4:129078000-129108000	Weak transcription	Gastric	stomach
10	chr4:129082800-129098400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129083600-129112600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:129083800-129102400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:129084800-129099400	Weak transcription	Liver	Liver
14	chr4:129084800-129104000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:129084800-129107800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:129084800-129112400	Weak transcription	NHDF-Ad	bronchial
17	chr4:129085200-129098000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:129085200-129098000	Weak transcription	HSMM	muscle
19	chr4:129085800-129105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:129089600-129102400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:129089600-129103400	Weak transcription	Fetal Intestine Large	intestine
22	chr4:129089800-129104000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:129090000-129104400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:129091600-129104000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:129092600-129107800	Weak transcription	Pancreas	Pancrea
26	chr4:129092600-129122000	Weak transcription	Esophagus	oesophagus
27	chr4:129093800-129096600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:129093800-129107800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:129094400-129107200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:129094600-129099600	Weak transcription	HepG2	liver
31	chr4:129094600-129107800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:129094600-129122200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:129094600-129131000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:129094800-129107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:129095000-129108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:129095000-129112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:129095800-129104200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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