Variant report

Variant	rs13142698
Chromosome Location	chr4:110348476-110348477
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	chr4:110346840..110352517-chr4:110352798..110357196,11	MCF-7	breast:
2	chr4:110346614..110351456-chr4:110352636..110356029,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247950	Chromatin interaction
ENSG00000138802	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10000545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10002595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10005355	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10016533	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs10155127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516558	0.92[CEU][hapmap];0.96[GIH][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098033	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11098035	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs11929713	0.83[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11930655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11933971	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934486	0.92[ASN][1000 genomes]
rs11935440	0.96[ASN][1000 genomes]
rs11935629	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11938593	0.96[ASN][1000 genomes]
rs11941344	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11942140	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11942858	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11942928	0.96[ASN][1000 genomes]
rs11943384	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs11943430	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs11944375	0.96[ASN][1000 genomes]
rs11944427	0.96[ASN][1000 genomes]
rs11944659	0.92[ASN][1000 genomes]
rs12639832	0.92[ASN][1000 genomes]
rs12640049	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12640161	1.00[ASN][1000 genomes]
rs12642304	0.94[ASN][1000 genomes]
rs12643055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12643844	0.94[ASN][1000 genomes]
rs12644055	0.96[ASN][1000 genomes]
rs12647695	0.96[ASN][1000 genomes]
rs12648138	1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs12648965	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650654	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs12650873	0.96[ASN][1000 genomes]
rs13103034	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13110999	0.85[CEU][hapmap]
rs13122093	0.85[CEU][hapmap]
rs13123618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125368	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13128124	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128221	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs13128445	0.85[MEX][hapmap]
rs13134239	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140373	0.85[CEU][hapmap]
rs13141701	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13143825	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13145066	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1509314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1509315	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17040410	0.96[ASN][1000 genomes]
rs17040436	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17040439	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17040461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17040488	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040510	0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040543	0.85[JPT][hapmap]
rs17585970	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs17619262	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs28521972	0.90[ASN][1000 genomes]
rs28681408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153531	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34224638	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34274964	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34377662	0.87[ASN][1000 genomes]
rs34441811	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34482781	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505473	0.88[EUR][1000 genomes]
rs34636377	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34836476	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35110951	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35359830	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35473144	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35594044	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35762958	0.94[ASN][1000 genomes]
rs35791246	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35940980	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36009064	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36115572	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775962	0.94[ASN][1000 genomes]
rs60957336	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61004219	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61242473	0.92[ASN][1000 genomes]
rs61439452	0.94[ASN][1000 genomes]
rs61553525	0.96[ASN][1000 genomes]
rs6533428	0.86[ASN][1000 genomes]
rs6533429	0.96[ASN][1000 genomes]
rs6533434	1.00[MEX][hapmap]
rs66642182	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66667140	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67473696	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68041341	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6812469	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815455	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs6817954	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818911	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6823032	0.94[ASN][1000 genomes]
rs6825928	0.88[MEX][hapmap]
rs6827006	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6833753	0.92[ASN][1000 genomes]
rs6835683	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837199	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845371	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848452	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6851517	0.96[ASN][1000 genomes]
rs6852037	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856291	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856446	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71603033	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72896619	1.00[ASN][1000 genomes]
rs72896622	1.00[ASN][1000 genomes]
rs72896625	1.00[ASN][1000 genomes]
rs72896629	1.00[ASN][1000 genomes]
rs72896632	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73838809	0.94[ASN][1000 genomes]
rs7436583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7436745	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs7440371	0.96[ASN][1000 genomes]
rs7440570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7675602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679836	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7680296	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7687245	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs9985632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9985964	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9994676	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9994985	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9999570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][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	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	esv1793428	chr4:110340134-110355591	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110328800-110353600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:110333200-110352800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:110333800-110353400	Weak transcription	HSMM	muscle
4	chr4:110334400-110351600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:110341400-110350000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:110341600-110353200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:110342200-110353600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:110343600-110350800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:110343800-110351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:110343800-110353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:110343800-110353600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:110344000-110349000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:110344000-110350600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:110344000-110350800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:110344000-110351000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:110344000-110351400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:110344000-110353000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:110344000-110353200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:110344000-110353200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:110344000-110353200	Weak transcription	Fetal Kidney	kidney
21	chr4:110344000-110353400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:110344000-110353400	Weak transcription	Liver	Liver
23	chr4:110344000-110353400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:110344000-110353400	Weak transcription	Osteobl	bone
25	chr4:110344000-110353600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:110344000-110353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:110344000-110353600	Weak transcription	Fetal Thymus	thymus
28	chr4:110344000-110353600	Weak transcription	NHDF-Ad	bronchial
29	chr4:110344000-110353800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:110344000-110353800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:110344000-110353800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:110344000-110353800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:110344200-110353400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:110344200-110353600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:110345200-110354200	Weak transcription	Ovary	ovary
36	chr4:110345600-110354000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:110346000-110348800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:110346000-110353400	Weak transcription	NH-A	brain
39	chr4:110346000-110354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:110346200-110350600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:110346200-110351400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:110346200-110353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:110346200-110353400	Weak transcription	Fetal Stomach	stomach
44	chr4:110346400-110351400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:110346800-110353400	Weak transcription	Fetal Intestine Large	intestine
46	chr4:110348200-110353000	Weak transcription	Fetal Lung	lung
47	chr4:110348200-110354000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:110348400-110353200	Weak transcription	HMEC	breast
49	chr4:110348400-110353600	Weak transcription	Primary T cells from cord blood	blood
50	chr4:110348400-110353800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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