Variant report

Variant	rs3791338
Chromosome Location	chr2:113945695-113945696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113875548..113877377-chr2:113943728..113946005,2	MCF-7	breast:
2	chr2:113943577..113946396-chr2:113947110..113948817,2	MCF-7	breast:
3	chr2:113944198..113947066-chr2:113955265..113958109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136689	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12614146	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3791335	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791336	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791337	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849167	0.80[AMR][1000 genomes]
rs4849168	0.89[CEU][hapmap];0.82[AMR][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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3791338	PSD4	cis	Whole Blood	GTEx
rs3791338	PSD4	cis	Esophagus Mucosa	GTEx
rs3791338	PSD4	cis	lung	GTEx
rs3791338	PSD4	cis	Esophagus Muscularis	GTEx
rs3791338	PSD4	cis	Skin Sun Exposed Lower leg	GTEx
rs3791338	PSD4	cis	Thyroid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113923000-113956000	Weak transcription	HMEC	breast
3	chr2:113934200-113949000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:113934400-113948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113934600-113946400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:113938800-113945800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:113939400-113946400	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr2:113939400-113946800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr2:113939400-113948400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:113939400-113949000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
14	chr2:113939600-113947800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:113939600-113953800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:113939600-113955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:113939600-113956200	Weak transcription	Fetal Lung	lung
18	chr2:113939800-113946200	Strong transcription	Thymus	Thymus
19	chr2:113940000-113946800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:113940400-113950000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:113940600-113945800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr2:113941000-113950000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:113941200-113949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:113941400-113950000	Weak transcription	Esophagus	oesophagus
26	chr2:113941600-113945800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:113941800-113949000	Genic enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:113941800-113950000	Weak transcription	NHEK	skin
29	chr2:113942000-113948800	Genic enhancers	Primary T cells from cord blood	blood
30	chr2:113942000-113950400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:113942400-113950200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:113942800-113956600	Strong transcription	Fetal Thymus	thymus
33	chr2:113942800-113961000	Strong transcription	Dnd41	blood
34	chr2:113943000-113946600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:113943000-113956200	Weak transcription	Brain Substantia Nigra	brain
36	chr2:113943600-113950000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:113943600-113956200	Weak transcription	Adipose Nuclei	Adipose
38	chr2:113943800-113948600	Weak transcription	Colonic Mucosa	Colon
39	chr2:113943800-113949600	Weak transcription	Gastric	stomach
40	chr2:113943800-113950000	Weak transcription	Lung	lung
41	chr2:113943800-113955200	Weak transcription	Stomach Mucosa	stomach
42	chr2:113943800-113956000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:113944200-113948400	Weak transcription	Liver	Liver
44	chr2:113944400-113945800	Genic enhancers	GM12878-XiMat	blood
45	chr2:113944400-113950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:113944400-113950000	Weak transcription	Placenta	Placenta
47	chr2:113944400-113950000	Weak transcription	Pancreas	Pancrea
48	chr2:113944600-113950000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:113945000-113945800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr2:113945000-113948600	Weak transcription	Fetal Intestine Small	intestine

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