Variant report

Variant	rs6044088
Chromosome Location	chr20:16517672-16517673
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004895	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1071913	0.85[JPT][hapmap]
rs16997837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997902	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2092695	0.85[JPT][hapmap]
rs2092696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143986	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2143987	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4440028	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814506	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4814507	0.84[JPT][hapmap]
rs4814508	0.85[JPT][hapmap]
rs6034522	0.85[JPT][hapmap]
rs6034523	0.84[JPT][hapmap]
rs6034524	0.85[JPT][hapmap]
rs6034531	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6034532	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6044080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6044082	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6044087	0.85[JPT][hapmap]
rs6044089	0.85[JPT][hapmap]
rs6044090	0.84[JPT][hapmap];0.80[YRI][hapmap]
rs6044094	0.84[JPT][hapmap]
rs6044095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6044097	0.85[JPT][hapmap]
rs6044098	0.84[JPT][hapmap]
rs6044100	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6044102	0.84[JPT][hapmap]
rs6044110	0.85[JPT][hapmap]
rs6044113	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6075070	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6111174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6111177	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6135791	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6135794	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6135795	0.84[JPT][hapmap]
rs6514689	0.84[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6044088	C20orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16485800-16521200	Weak transcription	Right Ventricle	heart
2	chr20:16489200-16521000	Weak transcription	Spleen	Spleen
3	chr20:16492400-16517800	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:16492600-16528800	Weak transcription	Primary B cells from cord blood	blood
5	chr20:16493000-16521200	Weak transcription	Liver	Liver
6	chr20:16497600-16521600	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:16506200-16517800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:16507400-16527000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr20:16508000-16522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:16508400-16536800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr20:16509000-16522000	Weak transcription	Aorta	Aorta
12	chr20:16509200-16553000	Weak transcription	Primary T cells from cord blood	blood
13	chr20:16509600-16521600	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:16511200-16518400	Weak transcription	NHEK	skin
15	chr20:16511400-16518600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:16511400-16519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:16511400-16519800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:16511600-16522400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr20:16511600-16549000	Weak transcription	Colonic Mucosa	Colon
20	chr20:16511800-16518000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:16514400-16522000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:16516600-16520000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:16517400-16517800	Enhancers	Esophagus	oesophagus
24	chr20:16517400-16517800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr20:16517400-16518200	Enhancers	Fetal Intestine Small	intestine
26	chr20:16517400-16518200	Enhancers	Left Ventricle	heart
27	chr20:16517400-16518200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr20:16517400-16518200	Enhancers	Small Intestine	intestine
29	chr20:16517400-16518400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr20:16517400-16518400	Enhancers	Fetal Intestine Large	intestine
31	chr20:16517400-16518400	Enhancers	Lung	lung
32	chr20:16517400-16518400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr20:16517400-16518600	Enhancers	Psoas Muscle	Psoas
34	chr20:16517400-16520200	Enhancers	Adipose Nuclei	Adipose
35	chr20:16517400-16521000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr20:16517600-16518000	Enhancers	Ovary	ovary
37	chr20:16517600-16518200	Enhancers	Duodenum Mucosa	Duodenum
38	chr20:16517600-16518200	Enhancers	HepG2	liver
39	chr20:16517600-16518400	Enhancers	Right Atrium	heart
40	chr20:16517600-16518600	Enhancers	Pancreas	Pancrea
41	chr20:16517600-16518800	Enhancers	Stomach Mucosa	stomach

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