Variant report

Variant	rs7583629
Chromosome Location	chr2:169672879-169672880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16855794	1.00[CHD][hapmap]
rs17200279	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs514629	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.94[EUR][1000 genomes]
rs829957	0.90[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[EUR][1000 genomes]
rs829958	0.90[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7583629	GALNT3	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169660000-169676000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:169660000-169688200	Weak transcription	Placenta	Placenta
3	chr2:169661400-169676800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:169662600-169673000	Weak transcription	Left Ventricle	heart
5	chr2:169662600-169675600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:169668400-169674000	Strong transcription	K562	blood
7	chr2:169669400-169673000	Weak transcription	Fetal Intestine Large	intestine
8	chr2:169670000-169698000	Weak transcription	Stomach Mucosa	stomach
9	chr2:169670200-169690200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:169670600-169690800	Weak transcription	Fetal Stomach	stomach
11	chr2:169671000-169676000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:169671200-169673600	Enhancers	Fetal Heart	heart
13	chr2:169671600-169673000	Enhancers	Adipose Nuclei	Adipose
14	chr2:169671600-169673200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:169671600-169673600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:169671600-169674000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:169671800-169673200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:169672200-169673400	Enhancers	Pancreas	Pancrea
19	chr2:169672200-169673800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:169672200-169675600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:169672200-169675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:169672400-169673200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:169672400-169673200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:169672400-169673400	Genic enhancers	Gastric	stomach
25	chr2:169672400-169674000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:169672400-169675600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:169672600-169673200	Enhancers	Right Atrium	heart
28	chr2:169672600-169673400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:169672600-169673400	Enhancers	Lung	lung
30	chr2:169672600-169673400	Enhancers	Right Ventricle	heart
31	chr2:169672600-169673400	Enhancers	NHLF	lung
32	chr2:169672600-169673800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:169672600-169673800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:169672600-169673800	Enhancers	NHDF-Ad	bronchial
35	chr2:169672600-169673800	Enhancers	Osteobl	bone
36	chr2:169672600-169675800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:169672600-169676800	Strong transcription	Fetal Intestine Small	intestine
38	chr2:169672800-169673000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:169672800-169673600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:169672800-169673600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:169672800-169673800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:169672800-169673800	Enhancers	HMEC	breast
43	chr2:169672800-169673800	Enhancers	NHEK	skin
44	chr2:169672800-169674000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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