Variant report

Variant	rs686226
Chromosome Location	chr1:168678914-168678915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:168675092..168677492-chr1:168677685..168680071,3	MCF-7	breast:
2	chr1:168677538..168680486-chr1:169074816..169077592,4	MCF-7	breast:
3	chr1:168677511..168680234-chr1:169074127..169077716,6	MCF-7	breast:
4	chr1:168678083..168681596-chr1:168682656..168685020,3	MCF-7	breast:
5	chr1:168678469..168680348-chr1:168740561..168743159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs512129	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs523447	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524705	0.81[JPT][hapmap]
rs528953	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs529949	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs531706	0.90[ASN][1000 genomes]
rs533619	0.90[ASN][1000 genomes]
rs542149	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs545833	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs573418	0.90[ASN][1000 genomes]
rs581753	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586318	0.83[JPT][hapmap]
rs590033	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs590875	0.90[ASN][1000 genomes]
rs607484	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs612680	0.81[AMR][1000 genomes]
rs627406	0.81[JPT][hapmap]
rs631451	0.81[JPT][hapmap]
rs635954	0.90[ASN][1000 genomes]
rs6427145	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656529	0.81[AMR][1000 genomes]
rs678629	0.90[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	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs686226	ALDH9A1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168666000-168679000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:168676200-168681400	Weak transcription	Gastric	stomach
3	chr1:168676200-168682600	Weak transcription	Right Atrium	heart
4	chr1:168676400-168687400	Weak transcription	Ovary	ovary
5	chr1:168677000-168680600	Weak transcription	Pancreas	Pancrea
6	chr1:168677600-168679000	Enhancers	HSMMtube	muscle
7	chr1:168677600-168679600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:168677600-168679800	Enhancers	Fetal Heart	heart
9	chr1:168677600-168680200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:168677600-168680200	Enhancers	Fetal Intestine Small	intestine
11	chr1:168677600-168681000	Enhancers	Fetal Intestine Large	intestine
12	chr1:168677800-168679600	Enhancers	Fetal Stomach	stomach
13	chr1:168677800-168679600	Enhancers	Stomach Mucosa	stomach
14	chr1:168677800-168680200	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:168677800-168680200	Enhancers	NHEK	skin
16	chr1:168678000-168679400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:168678000-168679400	Enhancers	Adipose Nuclei	Adipose
18	chr1:168678000-168679400	Enhancers	HepG2	liver
19	chr1:168678000-168679400	Enhancers	NHDF-Ad	bronchial
20	chr1:168678000-168679600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:168678000-168679800	Flanking Active TSS	A549	lung
22	chr1:168678000-168680000	Enhancers	Colon Smooth Muscle	Colon
23	chr1:168678000-168681000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:168678200-168679600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:168678200-168681000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:168678200-168695600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:168678400-168679000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:168678400-168679200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:168678400-168679200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:168678400-168679200	Enhancers	Fetal Muscle Leg	muscle
31	chr1:168678400-168679200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr1:168678400-168679800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:168678600-168679000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:168678600-168679400	Enhancers	Fetal Kidney	kidney
35	chr1:168678800-168679000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:168678800-168679000	Enhancers	Esophagus	oesophagus
37	chr1:168678800-168679000	Enhancers	Right Ventricle	heart
38	chr1:168678800-168679200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:168678800-168679200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:168678800-168679200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:168678800-168679200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:168678800-168679200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:168678800-168679200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr1:168678800-168679200	Enhancers	Fetal Lung	lung
45	chr1:168678800-168679200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:168678800-168679200	Flanking Active TSS	Hela-S3	cervix
47	chr1:168678800-168679200	Flanking Active TSS	HMEC	breast
48	chr1:168678800-168679200	Flanking Active TSS	HSMM	muscle
49	chr1:168678800-168679200	Flanking Active TSS	NH-A	brain
50	chr1:168678800-168679200	Flanking Active TSS	Osteobl	bone

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