Variant report

Variant	rs6445624
Chromosome Location	chr3:51358019-51358020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1031925	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865970	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1383251	0.85[EUR][1000 genomes]
rs1480354	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1552074	0.82[AMR][1000 genomes]
rs2127655	0.84[EUR][1000 genomes]
rs4428169	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4974105	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4974106	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445620	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6445622	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445628	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6773260	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6773332	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs751075	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7625006	0.84[EUR][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
rs6445624	TEX264	cis	Nerve Tibial	GTEx
rs6445624	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:19 , 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	chr3:51349400-51358600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:51351800-51367600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:51351800-51369200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:51352800-51369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:51353000-51370000	Weak transcription	Brain Germinal Matrix	brain
9	chr3:51353000-51370200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:51353200-51367600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:51353200-51370200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:51353400-51369400	Weak transcription	Fetal Brain Female	brain
13	chr3:51353400-51375800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
15	chr3:51353800-51367600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:51357400-51358200	Strong transcription	Brain Angular Gyrus	brain
17	chr3:51358000-51358200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:51358000-51358200	Bivalent/Poised TSS	Small Intestine	intestine
19	chr3:51358000-51376200	Weak transcription	HSMMtube	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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