Variant report

Variant	rs7617533
Chromosome Location	chr3:51355206-51355207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10433609	0.85[ASN][1000 genomes]
rs10446473	0.83[ASN][1000 genomes]
rs11130283	0.81[ASN][1000 genomes]
rs11130286	0.85[ASN][1000 genomes]
rs11130290	0.89[ASN][1000 genomes]
rs11706571	0.85[ASN][1000 genomes]
rs11711643	0.83[ASN][1000 genomes]
rs12632046	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12715446	0.85[ASN][1000 genomes]
rs13064149	0.81[ASN][1000 genomes]
rs1318649	0.85[ASN][1000 genomes]
rs1383251	0.81[EUR][1000 genomes]
rs1480353	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1480360	0.85[ASN][1000 genomes]
rs1542574	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1996331	0.85[ASN][1000 genomes]
rs1996332	0.83[ASN][1000 genomes]
rs2101055	0.87[ASN][1000 genomes]
rs2164599	0.83[ASN][1000 genomes]
rs2170178	0.81[ASN][1000 genomes]
rs2219890	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219891	0.85[ASN][1000 genomes]
rs2241784	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2355945	0.83[ASN][1000 genomes]
rs2883812	0.87[ASN][1000 genomes]
rs36188265	0.81[ASN][1000 genomes]
rs4538365	0.85[ASN][1000 genomes]
rs4557148	0.84[ASN][1000 genomes]
rs4687800	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974092	0.83[ASN][1000 genomes]
rs4974094	0.82[ASN][1000 genomes]
rs4974099	0.83[ASN][1000 genomes]
rs4974104	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974108	0.88[ASN][1000 genomes]
rs62257481	0.81[ASN][1000 genomes]
rs62257499	0.83[ASN][1000 genomes]
rs6445577	0.83[ASN][1000 genomes]
rs6445578	0.83[ASN][1000 genomes]
rs6445601	0.87[ASN][1000 genomes]
rs6445604	0.87[ASN][1000 genomes]
rs6445611	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6445727	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6772668	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6783235	0.81[ASN][1000 genomes]
rs6796847	0.84[ASN][1000 genomes]
rs7614317	0.85[ASN][1000 genomes]
rs7616967	0.85[ASN][1000 genomes]
rs7625821	0.84[ASN][1000 genomes]
rs7630714	0.88[ASN][1000 genomes]
rs7633708	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7640083	0.89[ASN][1000 genomes]
rs7648012	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7649069	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs899750	0.83[ASN][1000 genomes]
rs9832074	0.83[ASN][1000 genomes]
rs9832672	0.85[ASN][1000 genomes]
rs9836464	0.85[ASN][1000 genomes]
rs9856566	0.81[ASN][1000 genomes]
rs9857598	0.83[ASN][1000 genomes]
rs9860403	0.81[ASN][1000 genomes]
rs9870281	0.85[ASN][1000 genomes]
rs9877188	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7617533	TEX264	cis	Nerve Tibial	GTEx
rs7617533	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51340000-51370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:51341600-51372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:51344200-51371800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:51345000-51356400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:51345600-51355400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:51345600-51358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:51348000-51356400	Weak transcription	HSMMtube	muscle
8	chr3:51349400-51358600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:51351800-51367600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:51351800-51369200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:51352800-51369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:51353000-51357400	Weak transcription	Brain Angular Gyrus	brain
13	chr3:51353000-51370000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:51353000-51370200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:51353200-51367600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:51353200-51370200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:51353400-51369400	Weak transcription	Fetal Brain Female	brain
18	chr3:51353400-51375800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
20	chr3:51353800-51367600	Weak transcription	Brain Cingulate Gyrus	brain

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