Variant report

Variant	rs7207125
Chromosome Location	chr17:67007014-67007015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10512523	0.95[CHB][hapmap]
rs11077858	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11077859	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11077860	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11077884	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11453	0.88[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11657541	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11871766	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs11871944	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12325889	0.95[CHB][hapmap]
rs12939564	0.90[ASN][1000 genomes]
rs12940103	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12942599	0.90[ASN][1000 genomes]
rs12943969	0.88[ASN][1000 genomes]
rs1541470	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16973495	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2191212	0.89[ASN][1000 genomes]
rs2191213	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302292	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302293	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302294	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs36096265	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4548939	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968983	0.88[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6501944	0.86[JPT][hapmap]
rs6501947	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7215642	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7217543	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7218871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066758	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs8068236	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8070285	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs8070357	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894490	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7207125	ABCA9	cis	parietal	SCAN
rs7207125	ABCA6	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66977800-67027400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:66980400-67009400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr17:66989800-67011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr17:67000000-67007400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr17:67000200-67044200	Weak transcription	Right Ventricle	heart
6	chr17:67001200-67009400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:67001200-67014600	Strong transcription	Adipose Nuclei	Adipose
8	chr17:67001600-67009600	Weak transcription	Fetal Muscle Leg	muscle
9	chr17:67001800-67010800	Weak transcription	Left Ventricle	heart
10	chr17:67002400-67013200	Weak transcription	Fetal Lung	lung
11	chr17:67003800-67030600	Weak transcription	Brain Angular Gyrus	brain
12	chr17:67004000-67023400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:67004400-67009200	Weak transcription	NHDF-Ad	bronchial
14	chr17:67004800-67009400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr17:67005800-67007600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:67005800-67007600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:67006000-67007600	Weak transcription	Liver	Liver
18	chr17:67006000-67009800	Weak transcription	Ovary	ovary
19	chr17:67006000-67013200	Weak transcription	Psoas Muscle	Psoas
20	chr17:67007000-67009200	Weak transcription	Hela-S3	cervix

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