Variant report

Variant	rs2444983
Chromosome Location	chr15:33443920-33443921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2444981	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2444982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28710924	0.82[ASN][1000 genomes]
rs4350544	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4369627	0.81[ASN][1000 genomes]
rs5002280	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6494907	0.94[ASN][1000 genomes]
rs6494908	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2444983	ADAD2	trans	brain	seeQTL
rs2444983	PDYN	trans	brain	seeQTL
rs2444983	LAMB3	trans	brain	seeQTL
rs2444983	LTBP4	trans	brain	seeQTL
rs2444983	FCER2	trans	brain	seeQTL
rs2444983	GPR3	trans	brain	seeQTL
rs2444983	DUSP2	trans	brain	seeQTL
rs2444983	MSC	trans	brain	seeQTL
rs2444983	ANXA8L2	trans	brain	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33427800-33445400	Weak transcription	Right Atrium	heart
2	chr15:33438400-33444800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:33438600-33449800	Weak transcription	NHEK	skin
4	chr15:33438800-33444600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:33439000-33445200	Weak transcription	Placenta	Placenta
6	chr15:33439000-33445200	Weak transcription	Lung	lung
7	chr15:33439000-33447200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:33441000-33444400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:33441000-33445200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:33441000-33445200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:33441000-33447000	Weak transcription	Fetal Thymus	thymus
12	chr15:33441200-33444400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:33441200-33444800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:33441200-33451800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:33441600-33444000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:33442200-33444000	Enhancers	Fetal Intestine Small	intestine
17	chr15:33442200-33444200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:33442200-33447600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:33442200-33447600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr15:33442600-33444400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:33442600-33444600	Weak transcription	HMEC	breast
22	chr15:33442600-33448000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:33442800-33444800	Weak transcription	Osteobl	bone
24	chr15:33442800-33445200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr15:33442800-33445400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:33442800-33447400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:33443000-33444400	Active TSS	Brain Hippocampus Middle	brain
28	chr15:33443000-33445600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:33443200-33445200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:33443400-33444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:33443400-33444200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:33443400-33444600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:33443400-33445200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:33443400-33445600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:33443400-33446200	Active TSS	Psoas Muscle	Psoas
36	chr15:33443600-33445000	Enhancers	HSMM	muscle
37	chr15:33443600-33445600	Weak transcription	Primary B cells from cord blood	blood
38	chr15:33443800-33447000	Weak transcription	Fetal Kidney	kidney
39	chr15:33443800-33450200	Weak transcription	Fetal Intestine Large	intestine

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