Variant report

Variant	rs12757160
Chromosome Location	chr1:85759668-85759669
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	chr1:85740595..85746052-chr1:85759606..85765261,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10158486	0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10493763	0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161562	0.89[JPT][hapmap]
rs11161599	0.82[AMR][1000 genomes]
rs12122816	0.82[AMR][1000 genomes]
rs12126112	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126141	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12134420	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12136214	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729231	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1498374	0.82[AMR][1000 genomes]
rs17382844	0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284798	0.85[LWK][hapmap]
rs34561661	0.84[AMR][1000 genomes]
rs35240561	0.84[AMR][1000 genomes]
rs6698331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71652692	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12757160	SPATA1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
3	chr1:85748600-85764000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:85750000-85761400	Weak transcription	Lung	lung
5	chr1:85750000-85762800	Weak transcription	Pancreas	Pancrea
6	chr1:85750400-85762800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85750800-85763800	Weak transcription	Primary B cells from cord blood	blood
8	chr1:85752200-85762800	Weak transcription	Aorta	Aorta
9	chr1:85752400-85760600	Weak transcription	Fetal Stomach	stomach
10	chr1:85755800-85763200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:85756000-85759800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:85756000-85762800	Enhancers	NHEK	skin
13	chr1:85756200-85759800	Weak transcription	HUVEC	blood vessel
14	chr1:85756400-85762600	Weak transcription	Stomach Mucosa	stomach
15	chr1:85756600-85763200	Weak transcription	GM12878-XiMat	blood
16	chr1:85757000-85762800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85757400-85760600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:85757600-85760600	Weak transcription	Osteobl	bone
19	chr1:85757600-85760800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:85757600-85760800	Weak transcription	NHDF-Ad	bronchial
21	chr1:85757800-85760000	Weak transcription	NH-A	brain
22	chr1:85757800-85760600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:85757800-85762400	Weak transcription	HSMM	muscle
24	chr1:85757800-85762600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:85758400-85759800	Weak transcription	NHLF	lung
26	chr1:85758400-85760600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:85758400-85760800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:85758400-85761000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:85758600-85763000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:85759000-85763000	Enhancers	HMEC	breast
31	chr1:85759200-85760200	Enhancers	Esophagus	oesophagus
32	chr1:85759200-85763400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:85759400-85761200	Weak transcription	Spleen	Spleen
34	chr1:85759600-85765200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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