Variant report

Variant	rs10234384
Chromosome Location	chr7:104127901-104127902
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10216261	0.87[MEX][hapmap]
rs1034574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11520992	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11772914	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11972050	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12705219	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs17137948	0.86[JPT][hapmap]
rs6465992	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs6961457	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs6965697	0.86[JPT][hapmap]
rs7776632	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888925	chr7:104047599-104170560	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10234384	TRIM56	cis	parietal	SCAN
rs10234384	PIK3CG	cis	cerebellum	SCAN
rs10234384	FBXO24	cis	cerebellum	SCAN
rs10234384	AP1S1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104123600-104128000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:104127800-104128200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:104127800-104128200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:104127800-104128200	Enhancers	Brain Anterior Caudate	brain
5	chr7:104127800-104128400	Enhancers	Brain Germinal Matrix	brain
6	chr7:104127800-104128600	Enhancers	Rectal Mucosa Donor 31	rectum

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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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