Variant report

Variant	rs4927969
Chromosome Location	chr3:51203538-51203539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11130280	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080170	0.87[ASN][1000 genomes]
rs28708817	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28810453	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2883809	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35356497	0.87[ASN][1000 genomes]
rs4356848	0.89[ASN][1000 genomes]
rs4364203	0.82[ASN][1000 genomes]
rs4367100	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4434173	0.89[ASN][1000 genomes]
rs4475072	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4560329	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4572801	0.88[ASN][1000 genomes]
rs4927970	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4927973	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445501	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445549	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772197	0.90[ASN][1000 genomes]
rs6784455	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787805	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796642	0.83[ASN][1000 genomes]
rs6799722	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7618173	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815781	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9839484	0.87[ASN][1000 genomes]
rs9844581	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847479	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865532	0.89[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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4927969	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51168200-51210600	Weak transcription	Brain Angular Gyrus	brain
2	chr3:51183000-51209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:51183400-51206800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:51188800-51210600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:51189600-51206800	Weak transcription	Fetal Brain Female	brain
6	chr3:51190400-51205800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:51192600-51208800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:51193200-51209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:51193600-51209800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:51195200-51210000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:51196000-51207400	Weak transcription	Fetal Brain Male	brain
12	chr3:51196000-51209800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:51196600-51210400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:51197400-51210600	Weak transcription	Left Ventricle	heart
15	chr3:51197600-51210600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:51197800-51210000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:51198200-51210000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:51198200-51210600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:51198400-51210600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:51198600-51210600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:51200200-51205800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:51201200-51210600	Weak transcription	Brain Substantia Nigra	brain

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