Variant report

Variant	rs3935374
Chromosome Location	chr9:16826766-16826767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2243836	0.84[AFR][1000 genomes]
rs2480924	0.84[AFR][1000 genomes]
rs55933102	0.87[EUR][1000 genomes]
rs7866334	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892651	chr9:16816755-16869240	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3935374	PGAM2	trans	brain	seeQTL
rs3935374	NUPR1	trans	brain	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16823800-16827800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:16823800-16828000	Enhancers	NHDF-Ad	bronchial
3	chr9:16823800-16828400	Enhancers	Colon Smooth Muscle	Colon
4	chr9:16823800-16828400	Enhancers	Fetal Lung	lung
5	chr9:16824200-16827200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:16824200-16827600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:16824200-16828400	Enhancers	HSMM	muscle
8	chr9:16824400-16826800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr9:16824400-16826800	Enhancers	Fetal Muscle Leg	muscle
10	chr9:16824400-16827000	Enhancers	Rectal Smooth Muscle	rectum
11	chr9:16824400-16827400	Enhancers	Fetal Kidney	kidney
12	chr9:16824400-16827600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:16824400-16827600	Enhancers	Fetal Stomach	stomach
14	chr9:16824400-16828600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:16824600-16827400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:16824800-16826800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:16824800-16828400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:16824800-16828400	Weak transcription	Psoas Muscle	Psoas
19	chr9:16824800-16828800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:16825000-16826800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr9:16825000-16827200	Weak transcription	Ovary	ovary
22	chr9:16825000-16828200	Weak transcription	Adipose Nuclei	Adipose
23	chr9:16825000-16828200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:16825000-16828400	Weak transcription	Fetal Intestine Small	intestine
25	chr9:16825000-16828600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:16825000-16828600	Weak transcription	Placenta	Placenta
27	chr9:16825000-16828800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:16825400-16828400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:16825400-16828600	Weak transcription	NHEK	skin
30	chr9:16825600-16828400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:16825800-16829000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:16826200-16826800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr9:16826200-16828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:16826200-16828400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:16826400-16827400	Weak transcription	Fetal Intestine Large	intestine
36	chr9:16826400-16827800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:16826400-16828000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:16826400-16828000	Enhancers	NHLF	lung
39	chr9:16826400-16828200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:16826400-16828200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:16826400-16828400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:16826400-16828400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:16826400-16828400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:16826400-16828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:16826400-16828400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:16826400-16828400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:16826400-16828400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:16826400-16828400	Enhancers	Osteobl	bone
49	chr9:16826400-16828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:16826600-16826800	Enhancers	NH-A	brain

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