Variant report

Variant	rs1401340
Chromosome Location	chr3:34299081-34299082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:34294305..34297993-chr3:34298599..34300564,3	K562	blood:
2	chr3:34288854..34291341-chr3:34298518..34300242,2	K562	blood:

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

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

rs_ID	r²[population]
rs12494048	0.93[EUR][1000 genomes]
rs1356609	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1401342	0.83[AMR][1000 genomes]
rs1401343	0.82[AMR][1000 genomes]
rs1554320	0.81[AMR][1000 genomes]
rs2336570	0.96[ASN][1000 genomes]
rs4563356	0.93[ASN][1000 genomes]
rs4577415	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678668	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678673	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678674	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56143593	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248525	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62248526	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62248528	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6771362	0.82[AMR][1000 genomes]
rs73054790	0.88[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
rs1401340	CTDSPL	cis	parietal	SCAN
rs1401340	DLEC1	cis	parietal	SCAN
rs1401340	TRIM72	trans	cerebellum	SCAN
rs1401340	SUSD5	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34295600-34300600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:34295800-34299400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:34295800-34300400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:34295800-34300600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:34296000-34304000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:34296200-34301000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:34296400-34300200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:34296600-34299200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:34296600-34300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:34297000-34301800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:34297800-34299800	Weak transcription	Fetal Heart	heart
12	chr3:34297800-34301400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:34298000-34299200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:34298000-34299600	Weak transcription	Fetal Thymus	thymus
15	chr3:34298000-34300000	Weak transcription	Fetal Brain Female	brain
16	chr3:34298000-34300600	Weak transcription	Thymus	Thymus
17	chr3:34298000-34300600	Weak transcription	Dnd41	blood
18	chr3:34298000-34301800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:34298000-34302000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:34298000-34302000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:34298200-34302000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:34298200-34302000	Weak transcription	Fetal Lung	lung
23	chr3:34298400-34302400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:34298600-34300000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:34298600-34300800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:34298600-34303600	Weak transcription	Aorta	Aorta
27	chr3:34298800-34299200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:34298800-34300000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:34298800-34300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:34299000-34300200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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