Variant report

Variant	rs4561584
Chromosome Location	chr19:37017620-37017621
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	FOS	chr19:37017525-37018145	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr19:37017532-37018116	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr19:37017532-37018087	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:37016297..37018434-chr19:37262581..37265198,2	K562	blood:
2	chr19:36628146..36630638-chr19:37017222..37019646,2	K562	blood:
3	chr19:37012845..37016384-chr19:37017166..37020287,4	K562	blood:

Variant related genes	Relation type
ENSG00000228629	TF binding region
ZNF260	TF binding region
ENSG00000254004	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs2052730	0.85[ASN][1000 genomes]
rs2912422	0.85[ASN][1000 genomes]
rs2912424	0.85[ASN][1000 genomes]
rs2912426	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912427	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2912428	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912431	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912434	0.88[ASN][1000 genomes]
rs2912436	0.87[ASN][1000 genomes]
rs2912437	0.87[ASN][1000 genomes]
rs2912438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945946	0.86[ASN][1000 genomes]
rs2945960	0.86[ASN][1000 genomes]
rs2945966	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945967	0.87[ASN][1000 genomes]
rs2945968	0.85[ASN][1000 genomes]
rs2945970	0.93[ASN][1000 genomes]
rs2945974	0.86[ASN][1000 genomes]
rs2945977	0.85[ASN][1000 genomes]
rs2945979	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945980	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945982	0.89[ASN][1000 genomes]
rs2945987	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945988	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967432	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967434	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2967441	0.87[ASN][1000 genomes]
rs2967448	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967449	0.93[ASN][1000 genomes]
rs2967450	0.93[ASN][1000 genomes]
rs2967451	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967452	0.84[ASN][1000 genomes]
rs2967456	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967457	0.85[ASN][1000 genomes]
rs2967468	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967471	0.84[ASN][1000 genomes]
rs2967474	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967475	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967505	0.93[ASN][1000 genomes]
rs2967542	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2967544	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3107237	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3107238	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3111554	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
6	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36999200-37018000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:37000000-37017800	ZNF genes & repeats	Liver	Liver
3	chr19:37001000-37018000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:37001600-37018200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:37002600-37018000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:37003200-37018000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr19:37003800-37018200	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:37003800-37018600	ZNF genes & repeats	A549	lung
9	chr19:37008600-37017800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37008600-37017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:37009000-37018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:37009200-37017800	Weak transcription	Right Ventricle	heart
13	chr19:37009400-37018400	Weak transcription	Stomach Mucosa	stomach
14	chr19:37011400-37018200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:37012000-37018400	Weak transcription	Gastric	stomach
16	chr19:37013400-37018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:37013600-37018000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:37014200-37017800	Weak transcription	Brain Anterior Caudate	brain
19	chr19:37014200-37017800	Weak transcription	Pancreas	Pancrea
20	chr19:37014400-37017800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:37014400-37017800	Weak transcription	Brain Angular Gyrus	brain
22	chr19:37014400-37017800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:37014400-37017800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr19:37014400-37017800	Weak transcription	HSMMtube	muscle
25	chr19:37014400-37017800	Weak transcription	NHLF	lung
26	chr19:37015200-37018000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr19:37015400-37018200	ZNF genes & repeats	GM12878-XiMat	blood
28	chr19:37015600-37018000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr19:37016200-37017800	Weak transcription	HMEC	breast
30	chr19:37016200-37017800	Weak transcription	NHDF-Ad	bronchial
31	chr19:37016200-37018400	Weak transcription	Placenta	Placenta
32	chr19:37016200-37018400	Weak transcription	Psoas Muscle	Psoas
33	chr19:37016400-37017800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:37016400-37017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:37016400-37017800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:37016400-37017800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:37016400-37017800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:37016400-37017800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:37016400-37017800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:37016400-37017800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:37016400-37017800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:37016400-37017800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:37016400-37017800	Weak transcription	HUVEC	blood vessel
44	chr19:37016400-37017800	Weak transcription	Osteobl	bone
45	chr19:37016400-37018400	Weak transcription	Left Ventricle	heart
46	chr19:37016600-37017800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:37016600-37017800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:37016600-37017800	Weak transcription	Colonic Mucosa	Colon
49	chr19:37016600-37018400	Weak transcription	Aorta	Aorta
50	chr19:37016600-37018400	Weak transcription	Fetal Thymus	thymus

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