Variant report

Variant	rs12980972
Chromosome Location	chr19:38528060-38528061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12973690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12980973	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34417240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34846275	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35445607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36106417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58236040	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6508757	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7508583	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110656	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304573	0.90[EUR][1000 genomes];0.84[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv911656	chr19:38505037-38539988	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38508600-38537000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38514600-38530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:38514800-38537000	Weak transcription	Colonic Mucosa	Colon
4	chr19:38516800-38536200	Weak transcription	Spleen	Spleen
5	chr19:38517000-38530800	Weak transcription	NHEK	skin
6	chr19:38517000-38537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:38521800-38537000	Weak transcription	Esophagus	oesophagus
8	chr19:38521800-38538400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:38521800-38538400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:38522000-38536600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:38522200-38529000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:38522200-38537200	Weak transcription	Thymus	Thymus
15	chr19:38522400-38528800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:38522600-38528600	Weak transcription	Fetal Brain Male	brain
17	chr19:38522800-38529000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:38523400-38528600	Genic enhancers	A549	lung
19	chr19:38523400-38529400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:38524400-38528800	Enhancers	Fetal Muscle Trunk	muscle
21	chr19:38524400-38538400	Weak transcription	Small Intestine	intestine
22	chr19:38524800-38528600	Enhancers	Brain Hippocampus Middle	brain
23	chr19:38525000-38530600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:38525200-38536400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:38525200-38536600	Weak transcription	Gastric	stomach
27	chr19:38525800-38537000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:38525800-38538000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:38526000-38529000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:38526000-38529000	Enhancers	Brain Anterior Caudate	brain
31	chr19:38526000-38529000	Enhancers	Pancreas	Pancrea
32	chr19:38526000-38537600	Weak transcription	Fetal Intestine Large	intestine
33	chr19:38526200-38528200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:38526200-38528200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr19:38526200-38529800	Strong transcription	Fetal Intestine Small	intestine
36	chr19:38526400-38528200	Enhancers	Brain Substantia Nigra	brain
37	chr19:38526400-38528200	Enhancers	Left Ventricle	heart
38	chr19:38526400-38528200	Enhancers	Psoas Muscle	Psoas
39	chr19:38526400-38528400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr19:38526400-38528800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38526400-38528800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:38526400-38529000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38526400-38529000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38526400-38529000	Enhancers	Fetal Muscle Leg	muscle
45	chr19:38526600-38528200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:38526600-38528400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr19:38526600-38528400	Enhancers	Brain Cingulate Gyrus	brain
48	chr19:38526600-38528400	Enhancers	Fetal Lung	lung
49	chr19:38526600-38528400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr19:38526600-38528800	Enhancers	HUES48 Cell Line	embryonic stem cell

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