Variant report

Variant	rs1356609
Chromosome Location	chr3:34303283-34303284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12494048	0.94[EUR][1000 genomes]
rs1356610	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401340	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1401342	0.83[AMR][1000 genomes]
rs1401343	0.82[AMR][1000 genomes]
rs1554320	0.81[AMR][1000 genomes]
rs2336570	0.94[ASN][1000 genomes]
rs4563356	0.95[ASN][1000 genomes]
rs4577415	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678673	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143593	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62248525	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248526	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62248528	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6771362	0.82[AMR][1000 genomes]
rs73054790	0.86[ASN][1000 genomes]

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	nsv1001599	chr3:34149575-34437701	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv536533	chr3:34149575-34437701	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv876682	chr3:34149814-34401451	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv916961	chr3:34203879-34506554	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1001752	chr3:34294343-34323331	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1356609	TRIM72	trans	cerebellum	SCAN
rs1356609	CTDSPL	cis	parietal	SCAN
rs1356609	DLEC1	cis	parietal	SCAN
rs1356609	SUSD5	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34296000-34304000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:34298600-34303600	Weak transcription	Aorta	Aorta
3	chr3:34299200-34305400	Enhancers	Fetal Intestine Large	intestine
4	chr3:34299600-34305200	Enhancers	Fetal Thymus	thymus
5	chr3:34300600-34305000	Enhancers	Dnd41	blood
6	chr3:34300600-34305200	Enhancers	Thymus	Thymus
7	chr3:34301200-34305400	Enhancers	Fetal Brain Male	brain
8	chr3:34301400-34303800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:34301400-34304000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:34301600-34305800	Enhancers	Fetal Heart	heart
11	chr3:34302000-34303800	Enhancers	Fetal Lung	lung
12	chr3:34302000-34306200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:34302000-34307000	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:34302000-34307000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:34302000-34309400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:34302200-34304000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:34302200-34305000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:34302400-34303400	Enhancers	Placenta	Placenta
19	chr3:34302400-34307800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:34302600-34303800	Weak transcription	Fetal Brain Female	brain
21	chr3:34302600-34304000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:34302600-34304200	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:34302600-34304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:34302600-34304600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:34302800-34303600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:34302800-34304000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:34303000-34303400	Weak transcription	Fetal Intestine Small	intestine
28	chr3:34303000-34303400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:34303000-34305800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:34303200-34303600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:34303200-34304400	Enhancers	GM12878-XiMat	blood
32	chr3:34303200-34305800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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