Variant report

Variant	rs2075992
Chromosome Location	chr1:171080485-171080486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1736556	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1736560	0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs1736561	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1736564	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736565	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736567	0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1736568	0.81[EUR][1000 genomes]
rs1795240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795241	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795243	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1795244	0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1795245	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1795248	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6608459	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6608461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7054564	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7056422	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2075992	ALDH9A1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171077600-171081800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:171079000-171081000	Enhancers	NHLF	lung
3	chr1:171079400-171080800	Genic enhancers	Liver	Liver
4	chr1:171079400-171080800	Enhancers	Right Atrium	heart
5	chr1:171079400-171081000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:171079600-171080600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:171079600-171080800	Enhancers	Fetal Muscle Leg	muscle
8	chr1:171079600-171082800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:171079800-171080800	Enhancers	Fetal Stomach	stomach
10	chr1:171079800-171081000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:171079800-171081000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:171079800-171081200	Enhancers	Adipose Nuclei	Adipose
13	chr1:171079800-171082000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:171080000-171080800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:171080000-171080800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:171080000-171081000	Enhancers	Osteobl	bone
17	chr1:171080000-171081400	Enhancers	Fetal Lung	lung
18	chr1:171080200-171083200	Weak transcription	Aorta	Aorta
19	chr1:171080400-171080800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:171080400-171081000	Weak transcription	Small Intestine	intestine
21	chr1:171080400-171081000	Bivalent Enhancer	NHDF-Ad	bronchial

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