Variant report

Variant	rs12402118
Chromosome Location	chr1:75915826-75915827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75913816..75916653-chr1:75939102..75941877,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11806471	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs11809429	0.86[CHB][hapmap]
rs1249783	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1249786	0.80[CHD][hapmap]
rs1249794	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1249797	0.82[CHD][hapmap]
rs1249807	0.82[CHD][hapmap]
rs1343519	0.80[CHB][hapmap]
rs1343520	0.87[CHB][hapmap]
rs1571983	0.86[JPT][hapmap]
rs17096860	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs17096877	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1778459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858627	0.81[CHD][hapmap]
rs1891902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1936358	0.84[CHD][hapmap]
rs2083868	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs211786	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2347214	0.84[CHD][hapmap]
rs2347217	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs2587042	0.81[CHD][hapmap]
rs2972005	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3845363	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs6657734	0.86[CHB][hapmap]
rs6676696	0.86[CHB][hapmap]
rs74089241	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1011915	chr1:75879330-75934553	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546581	chr1:75897055-75937429	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3359779	chr1:75914980-75939472	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12402118	ACADM	cis	cerebellum	SCAN
rs12402118	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL
rs12402118	SLC44A5	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75915800-75916200	Enhancers	K562	blood
2	chr1:75915800-75916400	Weak transcription	Pancreas	Pancrea

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