Variant report

Variant	rs4705040
Chromosome Location	chr5:146881381-146881382
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11167991	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11959608	0.97[EUR][1000 genomes]
rs12186397	0.99[EUR][1000 genomes]
rs12653303	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1432845	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56348704	1.00[EUR][1000 genomes]
rs57813393	1.00[EUR][1000 genomes]
rs59183728	0.97[EUR][1000 genomes]
rs67890710	0.99[EUR][1000 genomes]
rs6860091	0.98[EUR][1000 genomes]
rs726054	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72833356	1.00[EUR][1000 genomes]
rs72833358	0.98[EUR][1000 genomes]
rs72833362	0.99[EUR][1000 genomes]
rs72833367	0.99[EUR][1000 genomes]
rs72833377	0.98[EUR][1000 genomes]
rs73264243	0.99[EUR][1000 genomes]
rs73794776	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7726760	0.94[CEU][hapmap];0.98[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4705040	SH3TC2	cis	cerebellum	SCAN
rs4705040	POU4F3	cis	parietal	SCAN
rs4705040	SCGB3A2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146851800-146883000	Weak transcription	Psoas Muscle	Psoas
2	chr5:146864600-146883000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr5:146865200-146882600	Weak transcription	Fetal Stomach	stomach
4	chr5:146866800-146882600	Weak transcription	NHLF	lung
5	chr5:146866800-146883000	Weak transcription	Ovary	ovary
6	chr5:146870800-146883000	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:146871400-146886400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:146871600-146887200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:146872200-146882400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:146873000-146882600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:146873200-146887400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:146876400-146882600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:146878400-146883600	Weak transcription	Aorta	Aorta
14	chr5:146878800-146887200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:146879800-146887000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:146880400-146881400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:146880800-146882000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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Input of quick search could be:

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

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