Variant report

Variant	rs35940980
Chromosome Location	chr4:110454039-110454040
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	chr4:110353206..110355233-chr4:110452632..110454561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247950	Chromatin interaction
ENSG00000138802	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10000545	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10002595	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10005355	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155127	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516558	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098033	0.86[ASN][1000 genomes]
rs11098035	0.94[ASN][1000 genomes]
rs11929713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930655	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11933971	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11934486	0.86[ASN][1000 genomes]
rs11935440	0.90[ASN][1000 genomes]
rs11935629	0.86[ASN][1000 genomes]
rs11938593	0.90[ASN][1000 genomes]
rs11941344	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942140	0.86[ASN][1000 genomes]
rs11942291	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942858	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942928	0.90[ASN][1000 genomes]
rs11943384	0.90[ASN][1000 genomes]
rs11943430	0.90[ASN][1000 genomes]
rs11944375	0.90[ASN][1000 genomes]
rs11944427	0.90[ASN][1000 genomes]
rs11944659	0.86[ASN][1000 genomes]
rs12639832	0.86[ASN][1000 genomes]
rs12640049	0.86[ASN][1000 genomes]
rs12640161	0.94[ASN][1000 genomes]
rs12642304	1.00[ASN][1000 genomes]
rs12643055	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643844	1.00[ASN][1000 genomes]
rs12644055	0.90[ASN][1000 genomes]
rs12647695	0.90[ASN][1000 genomes]
rs12648138	0.92[ASN][1000 genomes]
rs12648965	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650654	0.90[ASN][1000 genomes]
rs12650873	0.90[ASN][1000 genomes]
rs13103034	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13123618	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13125368	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128221	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13134239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141701	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142698	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13143825	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509314	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1509315	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17040410	0.90[ASN][1000 genomes]
rs17040436	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17040439	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17040461	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17040488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17585970	0.83[ASN][1000 genomes]
rs17619262	0.83[ASN][1000 genomes]
rs28521972	0.85[ASN][1000 genomes]
rs28681408	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34153531	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34224638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34274964	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34377662	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34441811	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34482781	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34505473	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34636377	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34836476	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35110951	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35359830	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35473144	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35594044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35762958	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35791246	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36009064	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36115572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775962	1.00[ASN][1000 genomes]
rs60957336	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61004219	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61242473	0.98[ASN][1000 genomes]
rs61439452	0.88[ASN][1000 genomes]
rs61553525	0.90[ASN][1000 genomes]
rs6533428	0.80[ASN][1000 genomes]
rs6533429	0.90[ASN][1000 genomes]
rs66642182	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66667140	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67473696	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68041341	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812469	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815455	0.94[ASN][1000 genomes]
rs6817954	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6818911	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823032	1.00[ASN][1000 genomes]
rs6827006	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833753	0.98[ASN][1000 genomes]
rs6835683	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837199	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6841198	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845371	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848452	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6851517	0.90[ASN][1000 genomes]
rs6852037	1.00[ASN][1000 genomes]
rs6856291	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856446	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71603033	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71623653	0.81[AMR][1000 genomes]
rs72896619	0.94[ASN][1000 genomes]
rs72896622	0.94[ASN][1000 genomes]
rs72896625	0.94[ASN][1000 genomes]
rs72896629	0.94[ASN][1000 genomes]
rs72896632	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73838809	1.00[ASN][1000 genomes]
rs7436583	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7436745	0.90[ASN][1000 genomes]
rs7440371	0.90[ASN][1000 genomes]
rs7440570	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7675602	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679836	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680296	0.85[EUR][1000 genomes]
rs9985632	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9985964	0.83[ASN][1000 genomes]
rs9994676	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994985	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999570	0.90[EUR][1000 genomes];1.00[ASN][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv525385	chr4:110395146-110466413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110393800-110469200	Weak transcription	Stomach Mucosa	stomach
2	chr4:110400200-110455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:110409400-110467800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:110411400-110464600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:110412400-110465400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:110412400-110466200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:110412400-110470600	Strong transcription	Fetal Thymus	thymus
8	chr4:110413400-110454800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:110416200-110454800	Weak transcription	Fetal Heart	heart
10	chr4:110417000-110455800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:110420200-110466400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:110423400-110454400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:110423400-110480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:110424600-110457000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:110424800-110456000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:110424800-110456600	Strong transcription	Osteobl	bone
17	chr4:110424800-110468400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:110425000-110463800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:110425200-110468000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:110425400-110464800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr4:110426600-110456800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:110427200-110454800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:110427400-110464800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:110428200-110464600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:110430400-110456600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:110433400-110465800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:110434600-110456200	Strong transcription	NH-A	brain
28	chr4:110434600-110456400	Strong transcription	Placenta	Placenta
29	chr4:110434800-110469600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr4:110435000-110456400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr4:110435000-110462600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:110435000-110468400	Strong transcription	Liver	Liver
33	chr4:110436800-110468000	Strong transcription	HSMM	muscle
34	chr4:110437600-110457200	Strong transcription	Fetal Lung	lung
35	chr4:110437600-110462600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:110442600-110455200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr4:110442600-110457200	Strong transcription	Fetal Intestine Large	intestine
38	chr4:110443800-110457000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:110445200-110463000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:110445400-110456600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:110445400-110456600	Strong transcription	Colon Smooth Muscle	Colon
42	chr4:110445400-110456600	Strong transcription	Dnd41	blood
43	chr4:110445400-110461800	Strong transcription	NHDF-Ad	bronchial
44	chr4:110445600-110456400	Strong transcription	Primary B cells from cord blood	blood
45	chr4:110445600-110456800	Strong transcription	HUVEC	blood vessel
46	chr4:110445600-110457000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr4:110445800-110457000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:110445800-110467800	Strong transcription	Adipose Nuclei	Adipose
49	chr4:110446000-110463000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:110446000-110464800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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