Variant report

Variant	rs2288344
Chromosome Location	chr15:56122347-56122348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1042477	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10851599	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11071228	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071231	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11630780	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11632096	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11632977	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11633263	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633313	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12102014	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102020	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12232351	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12898589	0.97[ASN][1000 genomes]
rs12910830	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13380185	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1509406	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs16976585	0.89[ASN][1000 genomes]
rs16976600	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1912398	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1912402	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2288345	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2414444	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28660477	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35040841	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56093337	0.82[AFR][1000 genomes]
rs56333939	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60482539	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60890210	0.87[ASN][1000 genomes]
rs66462353	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67505007	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7162435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175686	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7176225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7179116	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182397	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72732282	0.81[EUR][1000 genomes]
rs8024944	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028559	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8029247	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs8032158	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2288344	NEDD4	cis	lymphoblastoid	seeQTL
rs2288344	TCF12	cis	cerebellum	SCAN
rs2288344	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56095800-56128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56106000-56131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56112400-56124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:56112600-56123800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:56112600-56133600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:56114600-56128200	Weak transcription	Esophagus	oesophagus
7	chr15:56115400-56122400	Weak transcription	Aorta	Aorta
8	chr15:56115400-56148000	Weak transcription	Ovary	ovary
9	chr15:56115800-56129800	Weak transcription	Hela-S3	cervix
10	chr15:56116400-56122400	Weak transcription	Fetal Intestine Small	intestine
11	chr15:56116400-56124800	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:56116400-56129000	Weak transcription	NHLF	lung
13	chr15:56116400-56129600	Weak transcription	NHDF-Ad	bronchial
14	chr15:56116400-56133400	Weak transcription	Fetal Lung	lung
15	chr15:56116600-56122400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:56116600-56123800	Weak transcription	Adipose Nuclei	Adipose
17	chr15:56116600-56150600	Weak transcription	Right Ventricle	heart
18	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
19	chr15:56117200-56122400	Weak transcription	Fetal Stomach	stomach
20	chr15:56117600-56131200	Weak transcription	Small Intestine	intestine
21	chr15:56118000-56125800	Strong transcription	HSMM	muscle
22	chr15:56118600-56122400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:56118600-56151000	Weak transcription	Fetal Kidney	kidney
24	chr15:56118800-56147000	Weak transcription	Gastric	stomach
25	chr15:56118800-56149200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:56118800-56151400	Weak transcription	Brain Anterior Caudate	brain
27	chr15:56119200-56133000	Weak transcription	Primary T cells from cord blood	blood
28	chr15:56119400-56122600	Strong transcription	A549	lung
29	chr15:56119400-56123000	Enhancers	HMEC	breast
30	chr15:56119400-56124800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:56119400-56134800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:56120000-56125600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr15:56120000-56126200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:56120000-56136800	Strong transcription	Liver	Liver
35	chr15:56120000-56144800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:56120000-56147800	Weak transcription	HepG2	liver
37	chr15:56120200-56125600	Strong transcription	NH-A	brain
38	chr15:56120200-56125800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:56120200-56126400	Strong transcription	Osteobl	bone
40	chr15:56120600-56127600	Weak transcription	Lung	lung
41	chr15:56120600-56146600	Weak transcription	Pancreas	Pancrea
42	chr15:56120800-56126600	Weak transcription	Psoas Muscle	Psoas
43	chr15:56120800-56147200	Weak transcription	Thymus	Thymus
44	chr15:56121200-56147200	Weak transcription	Spleen	Spleen
45	chr15:56121400-56123200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:56121600-56122600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:56121600-56122600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:56121600-56122800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:56121600-56122800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:56121600-56123000	Enhancers	Dnd41	blood

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