Variant report

Variant	rs738200
Chromosome Location	chr22:28792887-28792888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10212083	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10483151	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12165708	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166129	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12166363	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12166475	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12167667	0.92[EUR][1000 genomes]
rs12167735	0.81[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12168708	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168851	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12169595	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12169966	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12170637	0.91[CEU][hapmap]
rs1297607	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134194	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs134197	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs134488	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134506	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134514	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs134524	0.91[CEU][hapmap]
rs134547	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs1474961	0.91[EUR][1000 genomes]
rs16986398	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs16986509	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17413461	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17487463	0.91[CEU][hapmap]
rs2013784	0.91[CEU][hapmap]
rs2144922	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs55738739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56391942	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57871917	0.87[AMR][1000 genomes]
rs59262169	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60042154	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6005807	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6519753	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7289625	0.91[CEU][hapmap]
rs7291268	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73430123	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73430136	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73430155	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73430186	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73437900	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73439811	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs738627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8137200	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8137808	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306457	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620778	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9620779	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9620797	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620799	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620803	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620804	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620809	0.92[EUR][1000 genomes]
rs9625433	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9625437	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9625438	0.91[CEU][hapmap]
rs9625440	0.91[CEU][hapmap]
rs9625447	0.91[CEU][hapmap]
rs9625467	1.00[CEU][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]
rs9625475	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625477	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9625478	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625481	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9625484	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625487	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625492	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625501	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625508	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625510	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9625515	0.91[EUR][1000 genomes]
rs9625516	0.92[EUR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs738200	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28789600-28794000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr22:28789800-28794600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr22:28789800-28794600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr22:28789800-28796200	Enhancers	Fetal Lung	lung
5	chr22:28790400-28793000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr22:28790400-28793600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:28790400-28794600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:28790400-28795400	Enhancers	Brain Substantia Nigra	brain
9	chr22:28790600-28793000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr22:28790600-28793200	Enhancers	Osteobl	bone
11	chr22:28790600-28793800	Enhancers	NHLF	lung
12	chr22:28790600-28794200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr22:28790600-28794200	Enhancers	NHDF-Ad	bronchial
14	chr22:28790600-28795600	Enhancers	Ovary	ovary
15	chr22:28791000-28793400	Weak transcription	Fetal Kidney	kidney
16	chr22:28791000-28793800	Enhancers	Brain Germinal Matrix	brain
17	chr22:28791200-28793600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr22:28791400-28793000	Enhancers	Fetal Intestine Small	intestine
19	chr22:28791400-28793000	Enhancers	HepG2	liver
20	chr22:28791400-28793400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:28791400-28800400	Weak transcription	Fetal Muscle Leg	muscle
22	chr22:28791600-28793000	Enhancers	Liver	Liver
23	chr22:28791600-28795400	Weak transcription	Lung	lung
24	chr22:28791600-28797600	Weak transcription	Placenta	Placenta
25	chr22:28791800-28793400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr22:28791800-28793600	Enhancers	Colon Smooth Muscle	Colon
27	chr22:28791800-28795200	Enhancers	Adipose Nuclei	Adipose
28	chr22:28791800-28795200	Enhancers	Dnd41	blood
29	chr22:28792000-28794600	Enhancers	Fetal Stomach	stomach
30	chr22:28792000-28795000	Enhancers	Brain Anterior Caudate	brain
31	chr22:28792000-28795200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr22:28792000-28795400	Enhancers	Brain Hippocampus Middle	brain
33	chr22:28792000-28795600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr22:28792200-28793000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr22:28792200-28793000	Enhancers	Aorta	Aorta
36	chr22:28792200-28793000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr22:28792200-28793400	Enhancers	Rectal Smooth Muscle	rectum
38	chr22:28792200-28794200	Enhancers	Fetal Heart	heart
39	chr22:28792200-28794800	Enhancers	Brain Angular Gyrus	brain
40	chr22:28792200-28795200	Enhancers	Brain Cingulate Gyrus	brain
41	chr22:28792400-28793000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:28792400-28793000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr22:28792400-28793200	Enhancers	Psoas Muscle	Psoas
44	chr22:28792400-28793200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr22:28792400-28795400	Enhancers	Fetal Brain Male	brain
46	chr22:28792600-28793400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr22:28792600-28793800	Weak transcription	Right Ventricle	heart
48	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:28792800-28793000	Enhancers	Gastric	stomach
50	chr22:28792800-28793000	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links