Variant report

Variant	rs939021
Chromosome Location	chr3:34298029-34298030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13063802	0.93[ASN][1000 genomes]
rs13079512	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13097138	0.93[ASN][1000 genomes]
rs1401341	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401344	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1401345	0.93[ASN][1000 genomes]
rs1518878	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1518879	0.93[ASN][1000 genomes]
rs1518888	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518891	0.94[ASN][1000 genomes]
rs1878862	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2139171	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34891554	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4267602	0.91[ASN][1000 genomes]
rs4514999	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4538327	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4678461	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4678462	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6793674	0.90[ASN][1000 genomes]
rs7631143	0.94[ASN][1000 genomes]
rs7642509	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883057	0.99[ASN][1000 genomes]
rs939022	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939023	0.98[ASN][1000 genomes]
rs9811006	0.92[CEU][hapmap]
rs9827191	0.94[ASN][1000 genomes]
rs9827539	0.95[ASN][1000 genomes]
rs9827879	0.81[AMR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs939021	DLEC1	cis	parietal	SCAN
rs939021	CMTM8	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr3:34296200-34298200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr3:34296200-34298600	Enhancers	Aorta	Aorta
8	chr3:34296200-34301000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:34296400-34300200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:34296600-34299200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:34296600-34300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:34297000-34298800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:34297000-34301800	Weak transcription	Fetal Intestine Small	intestine
14	chr3:34297400-34298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:34297400-34298200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr3:34297400-34298600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:34297600-34298400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:34297600-34298800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr3:34297600-34299000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:34297800-34298200	Enhancers	Fetal Lung	lung
21	chr3:34297800-34298800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:34297800-34299800	Weak transcription	Fetal Heart	heart
23	chr3:34297800-34301400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:34298000-34298400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:34298000-34298800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:34298000-34299200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:34298000-34299600	Weak transcription	Fetal Thymus	thymus
28	chr3:34298000-34300000	Weak transcription	Fetal Brain Female	brain
29	chr3:34298000-34300600	Weak transcription	Thymus	Thymus
30	chr3:34298000-34300600	Weak transcription	Dnd41	blood
31	chr3:34298000-34301800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:34298000-34302000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:34298000-34302000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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