Variant report

Variant	rs28538699
Chromosome Location	chr19:37967689-37967690
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37959263..37961865-chr19:37965726..37969534,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171827	Chromatin interaction
ENSG00000196437	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1015848	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1015849	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035479	0.88[EUR][1000 genomes]
rs10403582	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10403613	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404602	0.82[EUR][1000 genomes]
rs10404920	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10404945	0.85[EUR][1000 genomes]
rs10405064	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10405325	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10405407	0.81[EUR][1000 genomes]
rs10406177	0.91[EUR][1000 genomes]
rs10407084	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10409204	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10411574	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413602	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10414904	0.81[EUR][1000 genomes]
rs10415024	0.82[EUR][1000 genomes]
rs10415358	0.82[EUR][1000 genomes]
rs10415937	0.81[EUR][1000 genomes]
rs10417503	0.83[EUR][1000 genomes]
rs10417844	0.81[EUR][1000 genomes]
rs10420430	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420722	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10420754	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10422074	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422423	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10422667	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10422967	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10424574	0.82[EUR][1000 genomes]
rs10426618	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426666	0.82[EUR][1000 genomes]
rs10426699	0.82[EUR][1000 genomes]
rs11083426	0.89[EUR][1000 genomes]
rs12104381	0.81[EUR][1000 genomes]
rs12709813	0.81[EUR][1000 genomes]
rs12972252	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12979470	0.93[EUR][1000 genomes]
rs12981532	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13343471	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13343485	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13343502	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345116	0.81[EUR][1000 genomes]
rs13345148	0.81[EUR][1000 genomes]
rs1373991	0.81[EUR][1000 genomes]
rs1382357	0.95[EUR][1000 genomes]
rs1559229	0.82[EUR][1000 genomes]
rs2045908	0.95[EUR][1000 genomes]
rs2081096	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2112920	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112922	0.92[EUR][1000 genomes]
rs2112923	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2126977	0.90[EUR][1000 genomes]
rs2279148	0.88[EUR][1000 genomes]
rs2279149	0.88[EUR][1000 genomes]
rs2291004	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303131	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28373708	0.95[EUR][1000 genomes]
rs28402338	0.83[EUR][1000 genomes]
rs28605784	0.93[EUR][1000 genomes]
rs28623164	0.93[EUR][1000 genomes]
rs2891699	0.93[EUR][1000 genomes]
rs35085437	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35540940	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35777021	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745765	0.83[EUR][1000 genomes]
rs3760825	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3803895	0.88[EUR][1000 genomes]
rs4417644	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4452075	0.82[EUR][1000 genomes]
rs4801759	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801803	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802766	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802889	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803195	0.83[EUR][1000 genomes]
rs4803229	0.84[EUR][1000 genomes]
rs4803347	0.81[EUR][1000 genomes]
rs4803460	0.88[EUR][1000 genomes]
rs4803539	0.88[EUR][1000 genomes]
rs4969487	0.83[EUR][1000 genomes]
rs59224125	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508711	0.81[EUR][1000 genomes]
rs6508719	0.82[EUR][1000 genomes]
rs6508732	0.91[EUR][1000 genomes]
rs6508733	0.91[EUR][1000 genomes]
rs713256	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246993	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247259	0.81[EUR][1000 genomes]
rs7248733	0.89[EUR][1000 genomes]
rs7252099	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252325	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7252346	0.93[EUR][1000 genomes]
rs7253091	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7253114	0.92[EUR][1000 genomes]
rs7255140	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7255407	0.93[EUR][1000 genomes]
rs7255785	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7255952	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255972	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255996	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7256130	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7257495	0.81[EUR][1000 genomes]
rs7257672	0.81[EUR][1000 genomes]
rs7258692	0.82[EUR][1000 genomes]
rs7259968	0.81[EUR][1000 genomes]
rs73631095	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7408133	0.82[EUR][1000 genomes]
rs7408563	0.82[EUR][1000 genomes]
rs8106839	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109038	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8109632	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8111782	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8112610	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9304566	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9676739	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9676967	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9917081	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37961000-37967800	Weak transcription	Pancreas	Pancrea
2	chr19:37961000-37973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:37961000-37974000	Weak transcription	Stomach Mucosa	stomach
4	chr19:37961400-37970600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:37961400-37980400	ZNF genes & repeats	Liver	Liver
6	chr19:37961800-37967800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:37962200-37967800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr19:37962200-37968600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
9	chr19:37962200-37976200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37962200-37976400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:37962200-37977800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:37962200-37977800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:37962400-37968600	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr19:37962400-37977600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr19:37962400-37979200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:37962800-37968600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr19:37963000-37970000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
18	chr19:37963200-37969400	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:37963200-37976600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:37963200-37981000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:37963800-37969800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
22	chr19:37963800-37976400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr19:37963800-37985600	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:37964000-37968200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:37964000-37976400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr19:37964200-37977600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr19:37964400-37968600	Strong transcription	Left Ventricle	heart
28	chr19:37964800-37968000	Strong transcription	Brain Hippocampus Middle	brain
29	chr19:37964800-37968600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:37965200-37968200	Strong transcription	Fetal Thymus	thymus
31	chr19:37965200-37968600	ZNF genes & repeats	Thymus	Thymus
32	chr19:37965200-37968800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:37965200-37969000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr19:37965400-37968600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:37965400-37968600	ZNF genes & repeats	Fetal Intestine Large	intestine
36	chr19:37965400-37968600	Strong transcription	Fetal Stomach	stomach
37	chr19:37965600-37967800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:37965800-37971600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:37966000-37969400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:37966200-37968000	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr19:37966200-37968200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:37966200-37968200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:37966200-37968200	ZNF genes & repeats	A549	lung
44	chr19:37966200-37968400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:37966200-37969200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:37966200-37969200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:37966200-37970000	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr19:37966200-37970400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr19:37966200-37970400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
50	chr19:37966200-37976400	ZNF genes & repeats	Primary T cells from cord blood	blood

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