Variant report

Variant	rs10772338
Chromosome Location	chr12:7594354-7594355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10444429	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs10459096	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10772247	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10772330	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10772331	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10845124	0.86[AMR][1000 genomes]
rs10845176	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10845177	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10845178	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11053688	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs11053769	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs11053788	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12321231	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4072798	0.85[CEU][hapmap]
rs58195891	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	esv3350216	chr12:7432676-7604018	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10772338	CHD4	cis	parietal	SCAN
rs10772338	NDUFA9	cis	cerebellum	SCAN
rs10772338	MBL2	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:7592800-7595800	Weak transcription	Placenta	Placenta
2	chr12:7593000-7594800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:7593000-7596200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:7593000-7596800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:7593200-7595000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:7593400-7596400	Weak transcription	HUVEC	blood vessel
7	chr12:7594000-7595200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum

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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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