Variant report

Variant	rs2413975
Chromosome Location	chr15:50189303-50189304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1059851	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1059852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11630021	1.00[JPT][hapmap]
rs11632077	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11632116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11633571	1.00[JPT][hapmap]
rs11633714	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11633744	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11633759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11853881	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12914231	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12915207	1.00[JPT][hapmap]
rs13329598	1.00[JPT][hapmap]
rs16962994	1.00[JPT][hapmap]
rs16962999	1.00[JPT][hapmap]
rs17486425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17486446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17487811	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35996890	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4494482	1.00[JPT][hapmap]
rs4494483	1.00[JPT][hapmap]
rs4544192	1.00[JPT][hapmap]
rs6493383	1.00[JPT][hapmap]
rs7170482	1.00[JPT][hapmap]
rs7497350	1.00[JPT][hapmap]
rs8025533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8031452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8036570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8038434	1.00[JPT][hapmap]
rs8041979	1.00[JPT][hapmap]
rs8042458	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2413975	EIF3J	cis	parietal	SCAN
rs2413975	CEP152	cis	cerebellum	SCAN
rs2413975	TRPM7	cis	cerebellum	SCAN
rs2413975	SPG11	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:50163000-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:50167600-50200800	Weak transcription	Spleen	Spleen
7	chr15:50171200-50195200	Weak transcription	Placenta	Placenta
8	chr15:50180000-50193800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:50180200-50193800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:50180600-50190200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:50180600-50199400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr15:50182000-50199200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:50184600-50191600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:50186800-50189800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr15:50187600-50194400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:50187600-50195200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:50187800-50191400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:50187800-50192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:50187800-50192200	Weak transcription	Adipose Nuclei	Adipose
20	chr15:50187800-50192200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:50188200-50190200	Weak transcription	Brain Substantia Nigra	brain
22	chr15:50188200-50190200	Weak transcription	Fetal Lung	lung
23	chr15:50188200-50192000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:50188400-50190200	Weak transcription	Ovary	ovary
25	chr15:50188400-50190200	Weak transcription	NHDF-Ad	bronchial
26	chr15:50188400-50190600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr15:50188400-50190800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:50188400-50191200	Weak transcription	Fetal Kidney	kidney
29	chr15:50188400-50191400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:50188400-50192000	Weak transcription	Osteobl	bone
31	chr15:50188400-50194200	Weak transcription	Right Atrium	heart
32	chr15:50188600-50190000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr15:50188600-50190200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr15:50188600-50190200	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:50188600-50191200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:50188600-50191200	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:50188600-50191400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:50188600-50191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:50188600-50191400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:50188600-50191400	Weak transcription	HSMMtube	muscle
41	chr15:50188600-50192400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:50188600-50194000	Weak transcription	HSMM	muscle
43	chr15:50189000-50189400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:50189000-50189600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:50189200-50190200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:50189200-50190400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links