Variant report

Variant	rs16997877
Chromosome Location	chr20:16533162-16533163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12106039	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55987246	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6044114	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6135795	0.85[MKK][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16997877	TASP1	cis	parietal	SCAN
rs16997877	SEC23B	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16508400-16536800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:16509200-16553000	Weak transcription	Primary T cells from cord blood	blood
3	chr20:16511600-16549000	Weak transcription	Colonic Mucosa	Colon
4	chr20:16517800-16534200	Weak transcription	Esophagus	oesophagus
5	chr20:16518200-16535800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr20:16518800-16534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:16520200-16534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:16520400-16533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:16520400-16534800	Weak transcription	Fetal Intestine Small	intestine
10	chr20:16522200-16533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:16522800-16533800	Weak transcription	Right Ventricle	heart
12	chr20:16522800-16536800	Weak transcription	Aorta	Aorta
13	chr20:16523000-16533800	Weak transcription	Brain Anterior Caudate	brain
14	chr20:16523400-16535400	Weak transcription	Left Ventricle	heart
15	chr20:16524000-16533800	Weak transcription	Small Intestine	intestine
16	chr20:16528600-16534400	Weak transcription	Gastric	stomach
17	chr20:16529000-16533800	Weak transcription	Spleen	Spleen
18	chr20:16529200-16534400	Weak transcription	Pancreas	Pancrea
19	chr20:16529400-16534000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:16530200-16536400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:16530400-16536400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:16532000-16533200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr20:16532000-16533400	Enhancers	Fetal Thymus	thymus
24	chr20:16532000-16534000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:16532000-16534000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr20:16532200-16533200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr20:16532400-16533200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr20:16532400-16533200	Enhancers	Brain Angular Gyrus	brain
29	chr20:16532400-16533200	Enhancers	Ovary	ovary
30	chr20:16532400-16533400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:16532400-16533400	Enhancers	Lung	lung
32	chr20:16532600-16533200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr20:16532600-16533800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr20:16532600-16534000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:16532600-16534000	Weak transcription	Brain Substantia Nigra	brain
36	chr20:16532600-16535400	Weak transcription	Right Atrium	heart
37	chr20:16532800-16533200	Enhancers	Fetal Muscle Leg	muscle
38	chr20:16532800-16533400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr20:16532800-16534200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr20:16533000-16533200	Enhancers	Adipose Nuclei	Adipose
41	chr20:16533000-16533200	Enhancers	Brain Cingulate Gyrus	brain
42	chr20:16533000-16533400	Enhancers	Primary hematopoietic stem cells	blood
43	chr20:16533000-16533400	Enhancers	Placenta	Placenta
44	chr20:16533000-16534400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr20:16533000-16535000	Weak transcription	Psoas Muscle	Psoas
46	chr20:16533000-16535200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:16533000-16536000	Weak transcription	Fetal Kidney	kidney

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