Variant report

Variant	rs57090480
Chromosome Location	chr19:56789569-56789570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10775568	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11084440	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667369	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11670857	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11670870	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672079	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672081	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672220	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673002	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11883295	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12460523	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12461130	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17273365	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2869158	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3205192	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57731201	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58815584	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59503198	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59565427	0.81[EUR][1000 genomes]
rs59820036	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62122532	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62122534	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62122536	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252570	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73069662	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs758758	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs758760	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8101809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8103418	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8104291	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
4	nsv1058152	chr19:56703368-56805035	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv544093	chr19:56703368-56805035	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56729200-56803000	Weak transcription	Pancreas	Pancrea
2	chr19:56753000-56809000	Weak transcription	Gastric	stomach
3	chr19:56764400-56798600	Weak transcription	Placenta	Placenta
4	chr19:56764600-56799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:56764600-56804000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:56766600-56804200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:56768600-56794800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:56770200-56795200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:56770200-56799400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:56770400-56804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:56771200-56792000	Weak transcription	Aorta	Aorta
12	chr19:56771400-56817200	Weak transcription	Fetal Brain Male	brain
13	chr19:56771600-56807000	Weak transcription	Right Ventricle	heart
14	chr19:56772800-56807600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:56773000-56807400	Weak transcription	Esophagus	oesophagus
17	chr19:56773600-56790000	Weak transcription	Primary B cells from cord blood	blood
18	chr19:56775800-56815600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:56777000-56792800	Weak transcription	Fetal Intestine Large	intestine
20	chr19:56779600-56820200	Weak transcription	Hela-S3	cervix
21	chr19:56779800-56800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:56779800-56807200	Weak transcription	Left Ventricle	heart
23	chr19:56781400-56804600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:56782200-56799200	Weak transcription	Fetal Intestine Small	intestine
25	chr19:56782600-56794200	Weak transcription	K562	blood
26	chr19:56782800-56825200	Weak transcription	Psoas Muscle	Psoas
27	chr19:56783000-56825000	Weak transcription	Stomach Mucosa	stomach
28	chr19:56783200-56804000	Weak transcription	Brain Germinal Matrix	brain
29	chr19:56783200-56805400	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:56783400-56794000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr19:56784400-56794800	Weak transcription	NH-A	brain
32	chr19:56784800-56797600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:56785200-56798200	Weak transcription	Lung	lung
34	chr19:56785400-56803200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:56785400-56823600	Weak transcription	Osteobl	bone
36	chr19:56785600-56790000	Weak transcription	Fetal Stomach	stomach
37	chr19:56785600-56805400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:56785800-56802800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:56785800-56804000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:56786200-56804200	Weak transcription	Thymus	Thymus
41	chr19:56786800-56813000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:56788000-56804400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:56788200-56790400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:56788200-56794400	Weak transcription	HepG2	liver
45	chr19:56788200-56824400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:56788400-56789600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:56788600-56790200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:56788800-56790200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:56788800-56790600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:56788800-56793400	Weak transcription	Primary T cells from cord blood	blood

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