Variant report

Variant	rs2945980
Chromosome Location	chr19:37014669-37014670
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	chr19:37012845..37016384-chr19:37017166..37020287,4	K562	blood:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2385796	0.84[ASN][1000 genomes]
rs2912420	0.81[ASN][1000 genomes]
rs2912426	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912428	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912431	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2912438	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2945966	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945970	0.82[ASN][1000 genomes]
rs2945977	0.89[ASN][1000 genomes]
rs2945979	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945987	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945988	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967432	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967434	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2967448	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967449	0.81[ASN][1000 genomes]
rs2967450	0.81[ASN][1000 genomes]
rs2967451	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967456	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967467	0.82[ASN][1000 genomes]
rs2967468	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967474	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967475	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967505	0.81[ASN][1000 genomes]
rs2967542	0.84[ASN][1000 genomes]
rs2967544	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3107237	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3107238	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3111554	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4561584	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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:114 , 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	chr19:36999800-37017400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:37000000-37016400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:37000000-37017000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:37000000-37017800	ZNF genes & repeats	Liver	Liver
6	chr19:37001000-37018000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37001400-37017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:37001600-37016400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr19:37001600-37018200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:37002600-37018000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:37002800-37016400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:37002800-37016800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
13	chr19:37003200-37016800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:37003200-37017000	ZNF genes & repeats	Fetal Lung	lung
15	chr19:37003200-37018000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr19:37003400-37016800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr19:37003400-37017000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr19:37003400-37017200	ZNF genes & repeats	Dnd41	blood
19	chr19:37003400-37017400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:37003800-37017000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:37003800-37018200	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr19:37003800-37018600	ZNF genes & repeats	A549	lung
23	chr19:37004200-37015000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr19:37004600-37016400	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:37004600-37016600	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr19:37004600-37017400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:37004800-37016600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:37005000-37016400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr19:37005000-37016800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
30	chr19:37008600-37016400	Strong transcription	Osteobl	bone
31	chr19:37008600-37017800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:37008600-37017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:37008800-37015800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:37009000-37018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:37009200-37017800	Weak transcription	Right Ventricle	heart
36	chr19:37009400-37018400	Weak transcription	Stomach Mucosa	stomach
37	chr19:37010000-37016600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:37010000-37017600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr19:37010400-37017400	Weak transcription	Fetal Heart	heart
40	chr19:37011000-37016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:37011000-37016800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
42	chr19:37011200-37016600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr19:37011200-37017600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:37011400-37016400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:37011400-37016600	ZNF genes & repeats	Ovary	ovary
46	chr19:37011400-37016600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr19:37011400-37018200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:37011600-37014800	Weak transcription	NHDF-Ad	bronchial
49	chr19:37011600-37017200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr19:37012000-37018400	Weak transcription	Gastric	stomach

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