Variant report

Variant	rs12037869
Chromosome Location	chr1:85694986-85694987
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85694538..85697394-chr1:85706640..85709318,2	MCF-7	breast:
2	chr1:85665411..85671906-chr1:85683759..85698338,27	MCF-7	breast:
3	chr1:85694772..85696982-chr1:85723069..85725397,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162642	Chromatin interaction
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11161547	0.89[EUR][1000 genomes]
rs11161555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161558	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161563	0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs11161566	0.83[JPT][hapmap]
rs11161572	0.83[JPT][hapmap]
rs12124665	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12133263	0.83[JPT][hapmap]
rs12143319	0.83[JPT][hapmap]
rs12403276	0.88[MEX][hapmap]
rs12406129	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9433250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12037869	SYDE2	cis	parietal	SCAN
rs12037869	LOC339524	cis	parietal	SCAN
rs12037869	SPAG6	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85689400-85696000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:85690800-85696000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:85691400-85696200	Weak transcription	Right Ventricle	heart
5	chr1:85691600-85695200	Weak transcription	Pancreas	Pancrea
6	chr1:85691600-85695200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:85691600-85695600	Weak transcription	Left Ventricle	heart
8	chr1:85691600-85696000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:85691600-85696200	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:85691600-85696400	Weak transcription	Right Atrium	heart
11	chr1:85691800-85697000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:85692000-85695200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:85692000-85695400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:85692000-85695600	Weak transcription	Gastric	stomach
15	chr1:85692000-85696000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:85692000-85697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:85692200-85695400	Weak transcription	K562	blood
18	chr1:85692200-85697400	Weak transcription	NHEK	skin
19	chr1:85694200-85695200	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:85694200-85696400	Enhancers	Fetal Heart	heart
21	chr1:85694200-85696400	Enhancers	Fetal Lung	lung
22	chr1:85694600-85696600	Enhancers	Stomach Mucosa	stomach
23	chr1:85694800-85695400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:85694800-85696400	Enhancers	HepG2	liver

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