Variant report

Variant	rs12239097
Chromosome Location	chr1:75156257-75156258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10890139	0.93[ASN][1000 genomes]
rs11210495	0.93[ASN][1000 genomes]
rs11810971	0.87[AFR][1000 genomes]
rs1424663	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095729	0.91[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17095737	0.86[AFR][1000 genomes]
rs17095738	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17095739	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17095755	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575533	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv461995	chr1:75133142-75166623	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546578	chr1:75133142-75166623	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762153	chr1:75142205-75171211	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12239097	ACADM	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75141800-75179600	Weak transcription	Aorta	Aorta
2	chr1:75155400-75156400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:75155600-75156600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:75155600-75159200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:75155800-75156400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:75155800-75156400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:75156000-75158000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:75156000-75158800	Weak transcription	NH-A	brain
9	chr1:75156000-75167600	Weak transcription	Liver	Liver
10	chr1:75156000-75183400	Weak transcription	Fetal Heart	heart
11	chr1:75156200-75159000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:75156200-75167800	Weak transcription	Fetal Lung	lung
13	chr1:75156200-75168000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:75156200-75168200	Weak transcription	Ovary	ovary
15	chr1:75156200-75169200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:75156200-75169200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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