Variant report

Variant	rs41415947
Chromosome Location	chr3:52663577-52663578
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1344932	0.80[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17052269	0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17052322	0.80[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052355	0.80[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052424	0.80[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1971811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56815357	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57401769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57440640	1.00[AMR][1000 genomes]
rs57607481	0.88[AFR][1000 genomes]
rs57931767	0.85[AFR][1000 genomes]
rs58242587	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59078569	0.81[AFR][1000 genomes]
rs59410274	0.81[AFR][1000 genomes]
rs59789322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60351358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60404983	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60832323	1.00[AMR][1000 genomes]
rs61418167	0.81[AFR][1000 genomes]
rs61484330	1.00[AMR][1000 genomes]
rs6767229	0.91[AFR][1000 genomes]
rs6779626	0.94[AFR][1000 genomes]
rs6796577	0.88[AFR][1000 genomes]
rs6803865	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6809065	0.88[AFR][1000 genomes]
rs7615320	0.83[AFR][1000 genomes]
rs7616059	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7649820	0.94[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41415947	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52634800-52686000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr3:52636000-52703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52636000-52704000	Strong transcription	Placenta	Placenta
7	chr3:52636200-52703200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:52636600-52669200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:52636600-52673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52636600-52677400	Weak transcription	Pancreas	Pancrea
11	chr3:52636800-52703600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52639600-52670000	Strong transcription	Dnd41	blood
14	chr3:52640800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:52641000-52670800	Weak transcription	Stomach Mucosa	stomach
16	chr3:52641600-52664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52642400-52671000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:52642400-52676400	Weak transcription	Small Intestine	intestine
19	chr3:52642600-52711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:52643400-52691200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52643600-52677200	Weak transcription	Fetal Heart	heart
22	chr3:52643800-52682800	Weak transcription	K562	blood
23	chr3:52649400-52668800	Strong transcription	Primary B cells from cord blood	blood
24	chr3:52649800-52669800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:52651400-52666400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:52652800-52672400	Weak transcription	Gastric	stomach
28	chr3:52652800-52673600	Weak transcription	Aorta	Aorta
29	chr3:52653000-52671400	Weak transcription	Spleen	Spleen
30	chr3:52654000-52667600	Weak transcription	Colonic Mucosa	Colon
31	chr3:52654000-52669600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
33	chr3:52655400-52669200	Strong transcription	HSMM	muscle
34	chr3:52655600-52669400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:52655600-52680200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:52655600-52680200	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:52655800-52664800	Strong transcription	Thymus	Thymus
38	chr3:52655800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:52655800-52697600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:52655800-52704000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52656000-52683200	Strong transcription	Adipose Nuclei	Adipose
42	chr3:52656200-52666400	Weak transcription	Lung	lung
43	chr3:52656400-52664800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:52656400-52664800	Strong transcription	HUVEC	blood vessel
45	chr3:52656400-52665000	Strong transcription	Primary T cells from cord blood	blood
46	chr3:52656400-52669200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:52656400-52669400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52656600-52664600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:52656600-52669200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:52656600-52680200	Strong transcription	Fetal Muscle Trunk	muscle

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