Variant report

Variant	rs10433609
Chromosome Location	chr3:51311574-51311575
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10446473	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11130280	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11130283	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11130286	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11706571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11711643	0.99[ASN][1000 genomes]
rs11715606	0.86[ASN][1000 genomes]
rs12632046	0.81[ASN][1000 genomes]
rs12715446	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13064149	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13080170	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1318649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1480353	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1480360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1480362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1480364	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1996331	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1996332	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2061950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2101055	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2170178	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2219890	0.90[CHB][hapmap]
rs2219891	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2291162	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2355943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2355945	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2883809	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2883812	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36188265	0.94[ASN][1000 genomes]
rs3856932	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs4356848	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4367100	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs4475072	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4538365	1.00[ASN][1000 genomes]
rs4557148	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4560329	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4927970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4974092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4974094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4974099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4974104	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs4974108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62257481	0.96[ASN][1000 genomes]
rs62257499	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6445549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6445577	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6445578	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6445601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6445604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6445611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6772197	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6783235	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6784455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6787805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6796847	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7614317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7616967	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7617533	0.85[ASN][1000 genomes]
rs7630714	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7633708	0.95[CHB][hapmap]
rs7634799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7640083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7648012	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7649069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7651141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs899750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9832074	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9832672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9836464	1.00[ASN][1000 genomes]
rs9844581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9845500	0.84[ASN][1000 genomes]
rs9856566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9857598	0.99[ASN][1000 genomes]
rs9860403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9865532	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9870281	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs995543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10433609	TEX264	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
2	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:51296400-51318800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:51297000-51317400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:51298000-51314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:51298400-51319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:51303600-51312200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:51304400-51317400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:51305000-51318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:51308800-51314800	Weak transcription	Fetal Brain Female	brain
15	chr3:51309000-51313200	Enhancers	Primary T cells from cord blood	blood
16	chr3:51309200-51312400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:51309600-51311600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:51309600-51312000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:51309600-51312200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:51309800-51312000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:51309800-51312200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr3:51310200-51311800	Strong transcription	Brain Anterior Caudate	brain
23	chr3:51310400-51312200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:51310800-51311800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr3:51311000-51311600	Strong transcription	Brain Angular Gyrus	brain
26	chr3:51311000-51312000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:51311000-51312600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:51311200-51312400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:51311200-51319200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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