Variant report

Variant	rs59224125
Chromosome Location	chr19:37963205-37963206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr19:37963122-37963432	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37960401..37962298-chr19:37962534..37964930,2	MCF-7	breast:

Variant related genes	Relation type
ZNF569	TF binding region
ENSG00000171827	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1015848	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1015849	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1035479	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403582	0.93[EUR][1000 genomes]
rs10403613	0.81[EUR][1000 genomes]
rs10404920	0.82[EUR][1000 genomes]
rs10404945	0.86[EUR][1000 genomes]
rs10405064	0.83[EUR][1000 genomes]
rs10405325	0.86[EUR][1000 genomes]
rs10405407	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10406177	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10407084	0.91[EUR][1000 genomes]
rs10409204	0.93[EUR][1000 genomes]
rs10411574	0.91[EUR][1000 genomes]
rs10412043	0.81[EUR][1000 genomes]
rs10413602	0.88[EUR][1000 genomes]
rs10414904	0.82[EUR][1000 genomes]
rs10415937	0.82[EUR][1000 genomes]
rs10417503	0.81[EUR][1000 genomes]
rs10417844	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10420430	0.88[EUR][1000 genomes]
rs10420722	0.94[EUR][1000 genomes]
rs10420754	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422074	0.88[EUR][1000 genomes]
rs10422423	0.81[EUR][1000 genomes]
rs10422667	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10422967	0.81[EUR][1000 genomes]
rs10426618	0.95[EUR][1000 genomes]
rs11083426	0.86[EUR][1000 genomes]
rs11671972	0.89[ASN][1000 genomes]
rs12104380	0.81[EUR][1000 genomes]
rs12709813	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12972252	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12979470	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12981532	0.88[EUR][1000 genomes]
rs13343471	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13343485	0.82[EUR][1000 genomes]
rs13343502	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13345116	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1373991	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1382357	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1559229	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045908	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2081096	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112920	0.85[EUR][1000 genomes]
rs2112922	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112923	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126977	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279148	0.85[EUR][1000 genomes]
rs2279149	0.85[EUR][1000 genomes]
rs2291004	0.90[EUR][1000 genomes]
rs2303131	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28373708	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402338	0.81[EUR][1000 genomes]
rs28538699	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28605784	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28623164	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2891699	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35085437	0.81[EUR][1000 genomes]
rs35540940	0.90[EUR][1000 genomes]
rs35777021	0.93[EUR][1000 genomes]
rs3745765	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3760825	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803895	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417644	0.81[EUR][1000 genomes]
rs4452075	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4801759	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4801803	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802766	0.95[EUR][1000 genomes]
rs4802889	0.92[EUR][1000 genomes]
rs4803195	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803229	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803347	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803460	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803539	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4969487	0.81[EUR][1000 genomes]
rs62110394	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508711	0.82[EUR][1000 genomes]
rs6508719	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508732	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508733	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs713256	0.84[EUR][1000 genomes]
rs7246993	0.88[EUR][1000 genomes]
rs7247259	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248733	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252099	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7252325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252346	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253091	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253114	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7255407	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255785	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255952	0.93[EUR][1000 genomes]
rs7255972	0.93[EUR][1000 genomes]
rs7255996	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256130	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259968	0.82[EUR][1000 genomes]
rs73631095	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8106839	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109038	0.87[EUR][1000 genomes]
rs8109632	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111782	0.82[EUR][1000 genomes]
rs8112610	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304566	0.81[EUR][1000 genomes]
rs9676739	0.93[EUR][1000 genomes]
rs9676967	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917081	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37961000-37963800	Weak transcription	Colonic Mucosa	Colon
2	chr19:37961000-37964000	Weak transcription	Aorta	Aorta
3	chr19:37961000-37964400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:37961000-37965400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:37961000-37966800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:37961000-37967800	Weak transcription	Pancreas	Pancrea
7	chr19:37961000-37973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:37961000-37974000	Weak transcription	Stomach Mucosa	stomach
9	chr19:37961200-37964600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:37961200-37964600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:37961200-37967000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:37961400-37963800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:37961400-37963800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:37961400-37963800	Weak transcription	Psoas Muscle	Psoas
15	chr19:37961400-37963800	Weak transcription	Right Ventricle	heart
16	chr19:37961400-37964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:37961400-37964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:37961400-37964000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:37961400-37964000	Weak transcription	NHLF	lung
20	chr19:37961400-37964200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:37961400-37964600	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:37961400-37965800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:37961400-37966200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:37961400-37966200	Weak transcription	Osteobl	bone
25	chr19:37961400-37966600	Weak transcription	Brain Angular Gyrus	brain
26	chr19:37961400-37966600	Weak transcription	Placenta	Placenta
27	chr19:37961400-37966800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:37961400-37967000	Weak transcription	Fetal Heart	heart
29	chr19:37961400-37970600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:37961400-37980400	ZNF genes & repeats	Liver	Liver
31	chr19:37961600-37963600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:37961600-37963600	Weak transcription	Small Intestine	intestine
33	chr19:37961600-37964000	Weak transcription	Gastric	stomach
34	chr19:37961600-37966600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr19:37961800-37964000	Strong transcription	Thymus	Thymus
36	chr19:37961800-37967800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:37962200-37963400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:37962200-37963400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr19:37962200-37963400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:37962200-37963400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr19:37962200-37963400	Strong transcription	Fetal Intestine Large	intestine
42	chr19:37962200-37963400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr19:37962200-37963600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:37962200-37964000	Strong transcription	Left Ventricle	heart
45	chr19:37962200-37964000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr19:37962200-37964200	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:37962200-37964600	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr19:37962200-37965000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:37962200-37965000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:37962200-37965000	ZNF genes & repeats	Primary B cells from cord blood	blood

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