Variant report

Variant	rs1997902
Chromosome Location	chr20:16528288-16528289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004895	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1071913	0.85[JPT][hapmap]
rs16997837	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2092695	0.85[JPT][hapmap]
rs2092696	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143986	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2143987	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4440028	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4814506	0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][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];0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6034532	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6044080	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6044082	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6044087	0.85[JPT][hapmap]
rs6044088	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]
rs6044089	0.85[JPT][hapmap]
rs6044090	0.84[JPT][hapmap]
rs6044094	0.83[JPT][hapmap]
rs6044095	0.95[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]
rs6044096	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6044097	0.85[JPT][hapmap]
rs6044098	0.84[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs6044100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044102	0.84[JPT][hapmap]
rs6044104	0.89[AFR][1000 genomes]
rs6044110	0.85[JPT][hapmap]
rs6044113	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6075070	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6111174	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6111177	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135791	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6135794	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135795	0.84[JPT][hapmap]
rs6514689	0.84[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1997902	C20orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16492600-16528800	Weak transcription	Primary B cells from cord blood	blood
2	chr20:16508400-16536800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr20:16509200-16553000	Weak transcription	Primary T cells from cord blood	blood
4	chr20:16511600-16549000	Weak transcription	Colonic Mucosa	Colon
5	chr20:16517800-16534200	Weak transcription	Esophagus	oesophagus
6	chr20:16518200-16535800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:16518800-16534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:16520200-16532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:16520200-16534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:16520400-16533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:16520400-16534800	Weak transcription	Fetal Intestine Small	intestine
12	chr20:16522200-16533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:16522800-16528400	Weak transcription	Spleen	Spleen
14	chr20:16522800-16532400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:16522800-16533800	Weak transcription	Right Ventricle	heart
16	chr20:16522800-16536800	Weak transcription	Aorta	Aorta
17	chr20:16523000-16533800	Weak transcription	Brain Anterior Caudate	brain
18	chr20:16523400-16532600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:16523400-16535400	Weak transcription	Left Ventricle	heart
20	chr20:16523600-16528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:16523800-16532400	Weak transcription	Ovary	ovary
22	chr20:16524000-16533800	Weak transcription	Small Intestine	intestine
23	chr20:16525600-16532000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr20:16527800-16528400	Enhancers	Brain Angular Gyrus	brain
25	chr20:16527800-16528400	Enhancers	Pancreas	Pancrea
26	chr20:16528200-16528400	Enhancers	Lung	lung
27	chr20:16528200-16528600	Enhancers	Gastric	stomach
28	chr20:16528200-16528600	Enhancers	Psoas Muscle	Psoas
29	chr20:16528200-16529000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links