Variant report

Variant	rs12632533
Chromosome Location	chr3:48724599-48724600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs14018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4858800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4858830	1.00[CEU][hapmap]
rs4974088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap]
rs6766238	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs6796790	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs6801211	1.00[CEU][hapmap]
rs6806356	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9284885	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9859473	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs9879978	1.00[CEU][hapmap]
rs9882443	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs990211	0.82[CEU][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12632533	AMT	cis	cerebellum	SCAN
rs12632533	NICN1	cis	parietal	SCAN
rs12632533	DALRD3	cis	parietal	SCAN
rs12632533	DALRD3	cis	cerebellum	SCAN
rs12632533	QRICH1	cis	cerebellum	SCAN
rs12632533	ZNF589	cis	parietal	SCAN
rs12632533	WDR6	cis	cerebellum	SCAN
rs12632533	PHF7	cis	parietal	SCAN
rs12632533	P4HTM	cis	parietal	SCAN
rs12632533	QARS	cis	parietal	SCAN
rs12632533	WDR6	cis	parietal	SCAN
rs12632533	CDC25A	cis	cerebellum	SCAN
rs12632533	TLR9	cis	parietal	SCAN
rs12632533	NCKIPSD	cis	cerebellum	SCAN
rs12632533	IQCF1	cis	cerebellum	SCAN
rs12632533	AMT	cis	parietal	SCAN
rs12632533	NICN1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48718800-48725600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:48723600-48724800	Weak transcription	Aorta	Aorta
3	chr3:48723800-48724600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:48723800-48724600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:48723800-48724600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:48723800-48724600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:48723800-48724600	Enhancers	Adipose Nuclei	Adipose
8	chr3:48723800-48724600	Weak transcription	Esophagus	oesophagus
9	chr3:48723800-48724600	Weak transcription	Fetal Lung	lung
10	chr3:48723800-48724600	Enhancers	Placenta	Placenta
11	chr3:48723800-48724600	Weak transcription	Left Ventricle	heart
12	chr3:48723800-48724800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:48723800-48724800	Weak transcription	Gastric	stomach
14	chr3:48723800-48724800	Weak transcription	Lung	lung
15	chr3:48723800-48724800	Weak transcription	Pancreas	Pancrea
16	chr3:48723800-48724800	Enhancers	Right Ventricle	heart
17	chr3:48723800-48724800	Weak transcription	Hela-S3	cervix
18	chr3:48723800-48724800	Enhancers	HMEC	breast
19	chr3:48723800-48724800	Enhancers	NHLF	lung
20	chr3:48723800-48725000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:48723800-48725000	Weak transcription	Ovary	ovary
22	chr3:48723800-48725000	Weak transcription	NHDF-Ad	bronchial
23	chr3:48723800-48725400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:48723800-48725400	Enhancers	Fetal Heart	heart
25	chr3:48723800-48725600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:48723800-48732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:48724000-48724600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:48724000-48724600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:48724000-48724600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:48724000-48724600	Weak transcription	Primary T cells from cord blood	blood
32	chr3:48724000-48724600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:48724000-48724600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:48724000-48724600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:48724000-48724600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:48724000-48724600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:48724000-48724600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:48724000-48724600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:48724000-48724600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:48724000-48724600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:48724000-48724600	Weak transcription	Fetal Brain Female	brain
42	chr3:48724000-48724600	Weak transcription	Fetal Intestine Large	intestine
43	chr3:48724000-48724600	Weak transcription	Fetal Kidney	kidney
44	chr3:48724000-48724600	Enhancers	Fetal Muscle Leg	muscle
45	chr3:48724000-48724600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:48724000-48724600	Weak transcription	Thymus	Thymus
47	chr3:48724000-48724600	Enhancers	Dnd41	blood
48	chr3:48724000-48724600	Enhancers	NHEK	skin
49	chr3:48724000-48724800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:48724000-48724800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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