Variant report

Variant	rs9860962
Chromosome Location	chr3:51319389-51319390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12635282	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1383252	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1480355	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1480357	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1480358	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480363	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1480365	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1552072	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1552073	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1904786	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061951	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2355941	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2355942	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2883811	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34035394	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34251985	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4974093	0.89[AFR][1000 genomes]
rs4974095	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4974097	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974109	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67086923	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6782946	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6800805	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7634514	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs922612	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9683267	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814041	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9825454	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855442	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855454	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878100	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[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
rs9860962	TEX264	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:51313000-51322800	Weak transcription	HSMMtube	muscle
5	chr3:51313000-51323800	Weak transcription	Fetal Brain Male	brain
6	chr3:51313400-51321800	Weak transcription	Right Ventricle	heart
7	chr3:51313400-51322800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:51316000-51320600	Weak transcription	Fetal Brain Female	brain
10	chr3:51317000-51319800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:51317800-51320600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:51317800-51322200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:51318000-51322000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:51318200-51320600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:51318200-51320800	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:51318200-51328600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:51318600-51324400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:51318800-51319600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr3:51318800-51319600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:51319000-51319400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:51319000-51319600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr3:51319000-51319600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:51319000-51319600	Strong transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:51319000-51319800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr3:51319000-51320000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
26	chr3:51319200-51319400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr3:51319200-51319600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:51319200-51320000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:51319200-51320000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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